diff --git a/.gitignore b/.gitignore
index a6c390b..0e18c40 100644
--- a/.gitignore
+++ b/.gitignore
@@ -2,5 +2,4 @@ build
build.xml
manifest.mf
nbproject
-dist/README.TXT
-dist/NanoOK.jar
+dist/README.TXT
diff --git a/HDF5License.txt b/HDF5License.txt
new file mode 100644
index 0000000..b6eee1e
--- /dev/null
+++ b/HDF5License.txt
@@ -0,0 +1,92 @@
+
+Copyright Notice and License Terms for
+HDF5 (Hierarchical Data Format 5) Software Library and Utilities
+-----------------------------------------------------------------------------
+
+HDF5 (Hierarchical Data Format 5) Software Library and Utilities
+Copyright 2006-2015 by The HDF Group.
+
+NCSA HDF5 (Hierarchical Data Format 5) Software Library and Utilities
+Copyright 1998-2006 by the Board of Trustees of the University of Illinois.
+
+All rights reserved.
+
+Redistribution and use in source and binary forms, with or without
+modification, are permitted for any purpose (including commercial purposes)
+provided that the following conditions are met:
+
+1. Redistributions of source code must retain the above copyright notice,
+ this list of conditions, and the following disclaimer.
+
+2. Redistributions in binary form must reproduce the above copyright notice,
+ this list of conditions, and the following disclaimer in the documentation
+ and/or materials provided with the distribution.
+
+3. In addition, redistributions of modified forms of the source or binary
+ code must carry prominent notices stating that the original code was
+ changed and the date of the change.
+
+4. All publications or advertising materials mentioning features or use of
+ this software are asked, but not required, to acknowledge that it was
+ developed by The HDF Group and by the National Center for Supercomputing
+ Applications at the University of Illinois at Urbana-Champaign and
+ credit the contributors.
+
+5. Neither the name of The HDF Group, the name of the University, nor the
+ name of any Contributor may be used to endorse or promote products derived
+ from this software without specific prior written permission from
+ The HDF Group, the University, or the Contributor, respectively.
+
+DISCLAIMER:
+THIS SOFTWARE IS PROVIDED BY THE HDF GROUP AND THE CONTRIBUTORS
+"AS IS" WITH NO WARRANTY OF ANY KIND, EITHER EXPRESSED OR IMPLIED. In no
+event shall The HDF Group or the Contributors be liable for any damages
+suffered by the users arising out of the use of this software, even if
+advised of the possibility of such damage.
+
+-----------------------------------------------------------------------------
+-----------------------------------------------------------------------------
+
+Contributors: National Center for Supercomputing Applications (NCSA) at
+the University of Illinois, Fortner Software, Unidata Program Center (netCDF),
+The Independent JPEG Group (JPEG), Jean-loup Gailly and Mark Adler (gzip),
+and Digital Equipment Corporation (DEC).
+
+-----------------------------------------------------------------------------
+
+Portions of HDF5 were developed with support from the Lawrence Berkeley
+National Laboratory (LBNL) and the United States Department of Energy
+under Prime Contract No. DE-AC02-05CH11231.
+
+-----------------------------------------------------------------------------
+
+Portions of HDF5 were developed with support from the University of
+California, Lawrence Livermore National Laboratory (UC LLNL).
+The following statement applies to those portions of the product and must
+be retained in any redistribution of source code, binaries, documentation,
+and/or accompanying materials:
+
+ This work was partially produced at the University of California,
+ Lawrence Livermore National Laboratory (UC LLNL) under contract
+ no. W-7405-ENG-48 (Contract 48) between the U.S. Department of Energy
+ (DOE) and The Regents of the University of California (University)
+ for the operation of UC LLNL.
+
+ DISCLAIMER:
+ This work was prepared as an account of work sponsored by an agency of
+ the United States Government. Neither the United States Government nor
+ the University of California nor any of their employees, makes any
+ warranty, express or implied, or assumes any liability or responsibility
+ for the accuracy, completeness, or usefulness of any information,
+ apparatus, product, or process disclosed, or represents that its use
+ would not infringe privately- owned rights. Reference herein to any
+ specific commercial products, process, or service by trade name,
+ trademark, manufacturer, or otherwise, does not necessarily constitute
+ or imply its endorsement, recommendation, or favoring by the United
+ States Government or the University of California. The views and
+ opinions of authors expressed herein do not necessarily state or reflect
+ those of the United States Government or the University of California,
+ and shall not be used for advertising or product endorsement purposes.
+-----------------------------------------------------------------------------
+
+
diff --git a/bin/nanook b/bin/nanook
index 85b38a7..16fe060 100755
--- a/bin/nanook
+++ b/bin/nanook
@@ -2,16 +2,20 @@
JAVA_ARGS="-Xmx2048m"
-if [ -z "$NANOOK_SCRIPT_DIR" ] ; then
- echo "Error: You must set NANOOK_SCRIPT_DIR before running."
+if [ -z "$NANOOK_DIR" ] ; then
+ echo "Error: You must set NANOOK_DIR before running."
exit 1
fi
-JARFILE=${NANOOK_SCRIPT_DIR}/NanoOK.jar
+JARFILE=${NANOOK_DIR}/dist/NanoOK.jar
if [ ! -f ${JARFILE} ] ; then
- echo "Error: Can't find NanoOK.jar - it needs to be inside the directory pointed to by NANOOK_SCRIPT_DIR which is currently ${NANOOK_SCRIPT_DIR}"
+ echo "Error: Can't find NanoOK.jar - it needs to be inside the dist subdirectory of the directory pointed to by NANOOK_DIR which is currently ${NANOOK_DIR}"
exit 1
fi
+# If your library path (DYLD_LIBRARY_PATH on MAC) doesn't include HDF5 libraries,
+# you can manually set it here by adding a -Djava.library.path=/path/to/lib/dir
+# to the java command...
+
exec java ${JAVA_ARGS} -jar ${JARFILE} "$@"
diff --git a/bin/NanoOK.jar b/dist/NanoOK.jar
similarity index 67%
rename from bin/NanoOK.jar
rename to dist/NanoOK.jar
index fdee555..0243a93 100644
Binary files a/bin/NanoOK.jar and b/dist/NanoOK.jar differ
diff --git a/dist/README.TXT b/dist/README.TXT
new file mode 100644
index 0000000..f7bcf4a
--- /dev/null
+++ b/dist/README.TXT
@@ -0,0 +1,32 @@
+========================
+BUILD OUTPUT DESCRIPTION
+========================
+
+When you build an Java application project that has a main class, the IDE
+automatically copies all of the JAR
+files on the projects classpath to your projects dist/lib folder. The IDE
+also adds each of the JAR files to the Class-Path element in the application
+JAR files manifest file (MANIFEST.MF).
+
+To run the project from the command line, go to the dist folder and
+type the following:
+
+java -jar "NanoOK.jar"
+
+To distribute this project, zip up the dist folder (including the lib folder)
+and distribute the ZIP file.
+
+Notes:
+
+* If two JAR files on the project classpath have the same name, only the first
+JAR file is copied to the lib folder.
+* Only JAR files are copied to the lib folder.
+If the classpath contains other types of files or folders, these files (folders)
+are not copied.
+* If a library on the projects classpath also has a Class-Path element
+specified in the manifest,the content of the Class-Path element has to be on
+the projects runtime path.
+* To set a main class in a standard Java project, right-click the project node
+in the Projects window and choose Properties. Then click Run and enter the
+class name in the Main Class field. Alternatively, you can manually type the
+class name in the manifest Main-Class element.
diff --git a/dist/javadoc/allclasses-frame.html b/dist/javadoc/allclasses-frame.html
deleted file mode 100644
index 3e08caa..0000000
--- a/dist/javadoc/allclasses-frame.html
+++ /dev/null
@@ -1,57 +0,0 @@
-
-
-
-
-
-All Classes
-All Classes
-
-
-
diff --git a/dist/javadoc/allclasses-noframe.html b/dist/javadoc/allclasses-noframe.html
deleted file mode 100644
index 6b20369..0000000
--- a/dist/javadoc/allclasses-noframe.html
+++ /dev/null
@@ -1,57 +0,0 @@
-
-
-
-
-
-All Classes
-All Classes
-
-
-
diff --git a/dist/javadoc/constant-values.html b/dist/javadoc/constant-values.html
deleted file mode 100644
index 2d40d56..0000000
--- a/dist/javadoc/constant-values.html
+++ /dev/null
@@ -1,347 +0,0 @@
-
-
-
-
-
-Constant Field Values
-
-JavaScript is disabled on your browser.
-
-
-
-
-
-
-
-
-
-
nanook.*
-
-
-
-
-
-
-nanook.NanoOK
-Modifier and Type
-Constant Field
-Value
-
-
-
-
-
- public static final java.lang.StringVERSION_STRING "v0.23"
-
-
-
-
-
-
-
-
-nanook.ReadExtractorRunnable
-Modifier and Type
-Constant Field
-Value
-
-
-
-
-
- public static final java.lang.StringTYPE_STRING_2D "/Analyses/Basecall_2D_000/BaseCalled_2D/Fastq"
-
-
-
- public static final java.lang.StringTYPE_STRING_COMPLEMENT "/Analyses/Basecall_2D_000/BaseCalled_complement/Fastq"
-
-
-
- public static final java.lang.StringTYPE_STRING_TEMPLATE "/Analyses/Basecall_2D_000/BaseCalled_template/Fastq"
-
-
-
-
-
Deprecated List
-
-JavaScript is disabled on your browser.
-
-
-
-
-
-
-
-
-
-
-
-
diff --git a/dist/javadoc/help-doc.html b/dist/javadoc/help-doc.html
deleted file mode 100644
index e2dad81..0000000
--- a/dist/javadoc/help-doc.html
+++ /dev/null
@@ -1,215 +0,0 @@
-
-
-
-
-
-API Help
-
-JavaScript is disabled on your browser.
-
-
-
-
-
-
-
-
-
-Package
-Each package has a page that contains a list of its classes and interfaces, with a summary for each. This page can contain six categories:
-
-Interfaces (italic)
-Classes
-Enums
-Exceptions
-Errors
-Annotation Types
-
-
-
-Class/Interface
-Each class, interface, nested class and nested interface has its own separate page. Each of these pages has three sections consisting of a class/interface description, summary tables, and detailed member descriptions:
-
-Class inheritance diagram
-Direct Subclasses
-All Known Subinterfaces
-All Known Implementing Classes
-Class/interface declaration
-Class/interface description
-
-
-Nested Class Summary
-Field Summary
-Constructor Summary
-Method Summary
-
-
-Field Detail
-Constructor Detail
-Method Detail
-
-Each summary entry contains the first sentence from the detailed description for that item. The summary entries are alphabetical, while the detailed descriptions are in the order they appear in the source code. This preserves the logical groupings established by the programmer.
-
-
-Annotation Type
-Each annotation type has its own separate page with the following sections:
-
-Annotation Type declaration
-Annotation Type description
-Required Element Summary
-Optional Element Summary
-Element Detail
-
-
-
-Enum
-Each enum has its own separate page with the following sections:
-
-Enum declaration
-Enum description
-Enum Constant Summary
-Enum Constant Detail
-
-
-
-Use
-Each documented package, class and interface has its own Use page. This page describes what packages, classes, methods, constructors and fields use any part of the given class or package. Given a class or interface A, its Use page includes subclasses of A, fields declared as A, methods that return A, and methods and constructors with parameters of type A. You can access this page by first going to the package, class or interface, then clicking on the "Use" link in the navigation bar.
-
-
-Tree (Class Hierarchy)
-There is a Class Hierarchy page for all packages, plus a hierarchy for each package. Each hierarchy page contains a list of classes and a list of interfaces. The classes are organized by inheritance structure starting with java.lang.Object. The interfaces do not inherit from java.lang.Object.
-
-When viewing the Overview page, clicking on "Tree" displays the hierarchy for all packages.
-When viewing a particular package, class or interface page, clicking "Tree" displays the hierarchy for only that package.
-
-
-
-Deprecated API
-The Deprecated API page lists all of the API that have been deprecated. A deprecated API is not recommended for use, generally due to improvements, and a replacement API is usually given. Deprecated APIs may be removed in future implementations.
-
-
-Index
-The Index contains an alphabetic list of all classes, interfaces, constructors, methods, and fields.
-
-
-Prev/Next
-These links take you to the next or previous class, interface, package, or related page.
-
-
-Frames/No Frames
-These links show and hide the HTML frames. All pages are available with or without frames.
-
-
-All Classes
-The All Classes link shows all classes and interfaces except non-static nested types.
-
-
-Serialized Form
-Each serializable or externalizable class has a description of its serialization fields and methods. This information is of interest to re-implementors, not to developers using the API. While there is no link in the navigation bar, you can get to this information by going to any serialized class and clicking "Serialized Form" in the "See also" section of the class description.
-
-
-Constant Field Values
-The Constant Field Values page lists the static final fields and their values.
-
-
-
This help file applies to API documentation generated using the standard doclet. A-Index
-
-JavaScript is disabled on your browser.
-
-
-
-
-
-A B C D E F G I K L M N O P R S T V W
-
-
-
A
-
-addAlignment(Alignment) AlignmentMerger
-Merge in a new alignment
-
-addAlignmentStats(int, int, int, int, String, String) ReferenceSequenceStats
-Store alignment stats.
-
-addAllReferenceSections() ReportWriter
-Add sections for each reference sequence.
-
-addBase(int, int, int, int, int) SequenceLogo
-Set relative counts at a given position in the logo.
-
-addCoverage(int, int) ReferenceSequenceStats
-Increment coverage between two points.
-
-addDeletionError(int, String) ReadSetStats
-Store a deletion error.
-
-addDeletionError(int, String, ReadSetStats) ReferenceSequenceStats
-Store a deletion error.
-
-addDeletionMotifs(String) MotifStatistics
-Add a deletion motif.
-
-addInsertionError(int, String) ReadSetStats
-Store an insertion error.
-
-addInsertionError(int, String, ReadSetStats) ReferenceSequenceStats
-Store an insertion error.
-
-addInsertionMotifs(String) MotifStatistics
-Add a insertion motif.
-
-addkCounts(int, int[], int[]) AlignmentInfo
-addKmerAbundance(String, double, double) ReferenceSequenceStats
-addLength(String, int) ReadSetStats
-Store a read length in the array of read lengths.
-
-addLengthsSection() ReportWriter
-Add the read lengths section.
-
-addMotif(String) KmerMotifStatistic
-Add a motif to store.
-
-addMotifs(KmerMotifStatistic[], String) MotifStatistics
-Given a stretch of perfect sequence, store motifs at all k size.
-
-addPassFailSection() ReportWriter
-Add the pass/fail section
-
-addPerfectKmer(int) ReferenceSequenceStats
-Store all perfect kmer sizes for later analysis.
-
-addReadBestKmer(int) ReadSetStats
-Store best perfect kmers for each read.
-
-addReadBestKmer(int) ReferenceSequenceStats
-Store best perfect kmer length for each read.
-
-addReadFile(int) ReadSetStats
-Update count of read files.
-
-addReadSetStats(ReadSetStats) ReadLengthsSummaryFile
-Output read stats for a particular type (Template, Complement, 2D).
-
-addReadWithAlignment() ReadSetStats
-Store a read with an alignment.
-
-addReadWithoutAlignment() ReadSetStats
-Store a read without an alignment.
-
-addString(String) GCCounter
-Process sequence string
-
-addSubstitutionError(String, char, char) ReadSetStats
-Store a substitution error.
-
-addSubstitutionError(String, char, char, ReadSetStats) ReferenceSequenceStats
-Store a substitution error.
-
-addSubstitutionMotifs(String) MotifStatistics
-Add a substitution motif
-
-align() ReadAligner
-Alignment nanook
-Generic class to represent alignment
-
-Alignment(int, String, int, int, int, String, String, int, int, int, String, boolean) Alignment
-AlignmentFileParser nanook
-Interface for parsers of alignment files.
-
-AlignmentInfo nanook
-Class to hold information about an alignment.
-
-AlignmentInfo(String, int, String, int, int, int, int, int, int, int, int) AlignmentInfo
-Constructor.
-
-AlignmentMerger nanook
-Class to merge alignments
-
-AlignmentMerger(NanoOKOptions, ReferenceSequence, int, ReadSetStats, int) AlignmentMerger
-Constructor
-
-AlignmentsTableFile nanook
-Represents alignment summary file written by tool and used for graph plotting.
-
-AlignmentsTableFile(String) AlignmentsTableFile
-Constructor.
-
-
-
A B C D E F G I K L M N O P R S T V W L-Index
-
-JavaScript is disabled on your browser.
-
-
-
-
-
-A B C D E F G I K L M N O P R S T V W
-
-
-
L
-
-LastParser nanook
-Parser for LAST alignments
-
-LastParser(NanoOKOptions, References) LastParser
-loadReferences() References
-Load references
-
-
-
A B C D E F G I K L M N O P R S T V W M-Index
-
-JavaScript is disabled on your browser.
-
-
-
-
-
-A B C D E F G I K L M N O P R S T V W
-
-
-
M
-
-MAFAlignmentLine nanook
-Class representing an alignment line in a LAST file.
-
-MAFAlignmentLine(String) MAFAlignmentLine
-Constructor.
-
-MAFParser nanook
-Parser for LAST aligner files.
-
-MAFParser(NanoOKOptions, References) MAFParser
-Constructor.
-
-main(String[]) NanoOK
-Entry to tool.
-
-makePDF() ReportWriter
-MarginAlignParser nanook
-Parser for marginAlign files
-
-MarginAlignParser(NanoOKOptions, References) MarginAlignParser
-MAX_KMER NanoOKOptions
-MAX_READ_LENGTH NanoOKOptions
-MAX_READS NanoOKOptions
-MIN_ALIGNMENTS NanoOKOptions
-MODE_ALIGN NanoOKOptions
-MODE_ANALYSE NanoOKOptions
-MODE_EXTRACT NanoOKOptions
-MotifStatistics nanook
-Store all motif statistics (ie, insertion, deletion, substitution) at a range
- of sizes (3, 4, 5) for a single read type (Template, Complement or 2D).
-
-MotifStatistics() MotifStatistics
-Constructor
-
-
-
A B C D E F G I K L M N O P R S T V W N-Index
-
-JavaScript is disabled on your browser.
-
-
-
-
-
-A B C D E F G I K L M N O P R S T V W
-
-
-
N
-
-nanook - package nanook
-NanoOK nanook
-Entry class for tool.
-
-NanoOK() NanoOK
-NanoOKLog nanook
-Logging
-
-NanoOKLog() NanoOKLog
-NanoOKOptions nanook
-Representation of program options and some global constants.
-
-NanoOKOptions() NanoOKOptions
-
-
A B C D E F G I K L M N O P R S T V W O-Index
-
-JavaScript is disabled on your browser.
-
-
-
-
-
-A B C D E F G I K L M N O P R S T V W
-
-
-
O
-
-open(String) NanoOKLog
-open(String) ReadLengthsSummaryFile
-Open output file.
-
-open() ReportWriter
-Open the .tex file.
-
-openAlignmentsTableFile(String) ReferenceSequenceStats
-Create an alignments table file.
-
-openAlignmentSummaryFiles(String) ReferenceSequence
-Open alignment summary files for each reference for each type (Template, Complement, 2D).
-
-openLengthsFile() ReadSetStats
-Open a text file to store read lengths.
-
-options ReadExtractorRunnable
-outDir ReadExtractorRunnable
-outputAllMotifCounts() MotifStatistics
-Output motif counts for all types (debugging).
-
-outputMotifCounts() KmerMotifStatistic
-Write motif counts to stdout.
-
-outputMotifStats() ReadSetStats
-Write motif stats to screen.
-
-outputsToStdout() AlignmentFileParser
-Return true if this aligner outputs to Stdout and not a file
-
-outputsToStdout() BLASRParser
-outputsToStdout() BWAParser
-outputsToStdout() LastParser
-outputsToStdout() MarginAlignParser
-OverallStats nanook
-Represents overall (as opposed to per reference) stats for Template, Complement and 2D reads.
-
-OverallStats(NanoOKOptions) OverallStats
-Constructor.
-
-
-
A B C D E F G I K L M N O P R S T V W P-Index
-
-JavaScript is disabled on your browser.
-
-
-
-
-
-A B C D E F G I K L M N O P R S T V W
-
-
-
P
-
-parseArgs(String[]) NanoOKOptions
-Parse command line arguments.
-
-parseFile(String, AlignmentsTableFile, ReadSetStats) AlignmentFileParser
-Parse an alignment file.
-
-parseFile(String, AlignmentsTableFile, ReadSetStats) MAFParser
-Parse a LAST file.
-
-parseFile(String, AlignmentsTableFile, ReadSetStats) SAMParser
-ParserRunnable nanook
-Enables multi-threading of parsing
-
-ParserRunnable(NanoOKOptions, ReadSetStats, String, String, int, int, AlignmentsTableFile) ParserRunnable
-plot() RGraphPlotter
-Execute plot commands.
-
-print(String) NanoOKLog
-println(String) NanoOKLog
-printStats() ReadSetStats
-Print statistics to screen.
-
-ProcessLogger nanook
-Execute a system process and log result to a file
-
-ProcessLogger() ProcessLogger
-processReads() ReadSet
-Gather length statistics on reads and parse alignments
-
-processString() CIGARString
-
-
A B C D E F G I K L M N O P R S T V W R-Index
-
-JavaScript is disabled on your browser.
-
-
-
-
-
-A B C D E F G I K L M N O P R S T V W
-
-
-
R
-
-ReadAligner nanook
-Align reads
-
-ReadAligner(NanoOKOptions, AlignmentFileParser) ReadAligner
-Constructor
-
-ReadExtractor nanook
-Read extractor
-
-ReadExtractor(NanoOKOptions) ReadExtractor
-Constructor
-
-ReadExtractorRunnable nanook
-Enable multi-threading of read extraction
-
-ReadExtractorRunnable(NanoOKOptions, String, String, String) ReadExtractorRunnable
-ReadLengthsSummaryFile nanook
-Represents a summary file containing basic information on read lengths, N50 etc.
-
-ReadLengthsSummaryFile(String) ReadLengthsSummaryFile
-Constructor.
-
-ReadSet nanook
-Represents a read set (Template reads, Complement reads, or 2D reads).
-
-ReadSet(int, NanoOKOptions, ReadSetStats) ReadSet
-Constructor
-
-ReadSetStats nanook
-Represent statistics about a read set (for example Template read set).
-
-ReadSetStats(NanoOKOptions, int) ReadSetStats
-Constructor
-
-readSizesFile() References
-READTYPE_COMBINED NanoOKOptions
-READTYPE_FAIL NanoOKOptions
-READTYPE_PASS NanoOKOptions
-References nanook
-Represents the set of references (sequences) used for the analysis.
-
-References(NanoOKOptions) References
-Constructor
-
-ReferenceSequence nanook
-Represents a sequence (contig) within a reference.
-
-ReferenceSequence(String, int, String) ReferenceSequence
-Constructor
-
-ReferenceSequenceStats nanook
-Stores stats for each reference sequence, one object per read type (Template, Complement, 2D).
-
-ReferenceSequenceStats(int, String) ReferenceSequenceStats
-Constructor.
-
-ReportWriter nanook
-Writes a LaTeX report file.
-
-ReportWriter(NanoOKOptions, OverallStats) ReportWriter
-Constructor.
-
-RGraphPlotter nanook
-Executes command to plot graphs with R.
-
-RGraphPlotter(NanoOKOptions) RGraphPlotter
-Constructor.
-
-RGraphRunnable nanook
-Enable multi-threading of R plotting
-
-RGraphRunnable(String, List<String>, String) RGraphRunnable
-run() ParserRunnable
-Entry point to thread
-
-run() ReadExtractorRunnable
-Extract reads of each type from file
-
-run() RGraphRunnable
-run() SystemCommandRunnable
-runAndLogCommand(String, String, boolean) ProcessLogger
-runCommand(String) ProcessLogger
-runScript(String, String, String) RGraphPlotter
-
-
A B C D E F G I K L M N O P R S T V W S-Index
-
-JavaScript is disabled on your browser.
-
-
-
-
-
-A B C D E F G I K L M N O P R S T V W
-
-
-
S
-
-SAMParser nanook
-Parser for SAM format files.
-
-SAMParser(NanoOKOptions, References) SAMParser
-Parse a SAM file.
-
-saveImage(String) SequenceLogo
-Save the logo as an image.
-
-SequenceLogo nanook
-Create sequence logo (for error motifs etc.)
-
-SequenceLogo(int) SequenceLogo
-Constructor
-
-SequenceLogo() SequenceLogo
-Debugging constructor
-
-SequenceReader nanook
-Read FASTA files
-
-SequenceReader(boolean) SequenceReader
-setAlignmentParams(String) AlignmentFileParser
-Set alignment parameters to run executable
-
-setAlignmentParams(String) BLASRParser
-setAlignmentParams(String) BWAParser
-setAlignmentParams(String) LastParser
-setAlignmentParams(String) MarginAlignParser
-setHitStrand(String) Alignment
-setQueryStrand(String) Alignment
-setReadFormat(int) NanoOKOptions
-setWriteFormat(boolean, boolean, boolean) ProcessLogger
-sortAlignments() AlignmentFileParser
-Sort alignments by score
-
-sortAlignments() MAFParser
-Sort alignments in order of score
-
-sortAlignments() SAMParser
-Sort alignments in order of score
-
-sortKmerAbundance() ReferenceSequenceStats
-storeKmers(int, KmerTable) SequenceReader
-SystemCommandRunnable nanook
-Enable multi-threading of system commands
-
-SystemCommandRunnable(NanoOKOptions, String, String, String, String) SystemCommandRunnable
-Constructor
-
-
-
A B C D E F G I K L M N O P R S T V W T-Index
-
-JavaScript is disabled on your browser.
-
-
-
-
-
-A B C D E F G I K L M N O P R S T V W
-
-
-
T
-
-testLogo() NanoOK
-Test logo plotting
-
-testParser(NanoOKOptions, OverallStats, References) NanoOK
-Test parser
-
-testSequenceReader() NanoOK
-Test SequenceReader class
-
-TYPE_2D NanoOKOptions
-TYPE_ALL NanoOKOptions
-TYPE_BOTTOM KmerMotifStatistic
-TYPE_COMPLEMENT NanoOKOptions
-TYPE_DELETION NanoOKOptions
-TYPE_INSERTION NanoOKOptions
-TYPE_STRING_2D ReadExtractorRunnable
-TYPE_STRING_COMPLEMENT ReadExtractorRunnable
-TYPE_STRING_TEMPLATE ReadExtractorRunnable
-TYPE_SUBSTITUTION NanoOKOptions
-TYPE_TEMPLATE NanoOKOptions
-TYPE_TOP KmerMotifStatistic
-
-
A B C D E F G I K L M N O P R S T V W V-Index
-
-JavaScript is disabled on your browser.
-
-
-
-
-
-A B C D E F G I K L M N O P R S T V W
-
-
-
V
-
-VERSION_STRING NanoOK
-
-
A B C D E F G I K L M N O P R S T V W W-Index
-
-JavaScript is disabled on your browser.
-
-
-
-
-
-A B C D E F G I K L M N O P R S T V W
-
-
-
W
-
-writeAlignment(String, MAFAlignmentLine, MAFAlignmentLine, AlignmentInfo) AlignmentsTableFile
-Write an alignment line.
-
-writeAlignmentsSection(ReadSetStats) ReportWriter
-Write the alignments section to the report.
-
-writeBestPerfectKmerHist(String) ReferenceSequenceStats
-Write data for best perfect kmer histogram.
-
-writeBestPerfectKmerHistCumulative(String) ReferenceSequenceStats
-Write data for best perfect kmer cumulative histogram.
-
-writeCoverageData(String, int) ReferenceSequenceStats
-Write coverage file for later graph plotting.
-
-writeDeletionLogoImage(int, String, int) MotifStatistics
-Write deletion logo image (via KmerMotifStatistic object)
-
-writeDeletionStats(String) ReferenceSequenceStats
-Write a file of deletion stats for plotting.
-
-writeInsertionLogoImage(int, String, int) MotifStatistics
-Write insertion logo image (via KmerMotifStatistic object)
-
-writeInsertionStats(String) ReferenceSequenceStats
-Write a file of insertion stats for plotting.
-
-writekCounts(String, int, int, int[], int[]) ReadSetStats
-writeKmerFile(int, String) ReferenceSequence
-writeKmerTable() KmerTable
-writeLogoImage(int, String) KmerMotifStatistic
-Write a top 10 or bottom 10 logo image.
-
-writeMafFile(String) Alignment
-writeMergedAlignment(String, AlignmentMerger, AlignmentInfo) AlignmentsTableFile
-writeMotifRange(int, int, int) ReportWriter
-Write Top 10 or Bottom 10 moitf section.
-
-writeMotifSection() ReportWriter
-Write motif section of report.
-
-writeNoAlignmentMessage(String) AlignmentsTableFile
-Used when no alignment found for this query.
-
-writePerfectKmerHist(String) ReferenceSequenceStats
-Write data for perfect kmer histogram.
-
-writeReferenceSection(ReferenceSequence) ReportWriter
-Write a section for a reference sequence.
-
-writeReferenceStatFiles(int) References
-Initiate writing of all statistics data files used to generate graphs.
-
-writeReferenceSummary(int) References
-Write reference summary text file.
-
-writeReport() ReportWriter
-Write the LaTeX report.
-
-writeSubstitutionErrorsSection() ReportWriter
-Write section to report on substitution errors.
-
-writeSubstitutionLogoImage(int, String, int) MotifStatistics
-Write substitution logo image (via KmerMotifStatistic object)
-
-writeSummary(PrintWriter, String) ReferenceSequenceStats
-Write a line to the reference sequence summary file.
-
-writeSummaryFile(String) ReadSetStats
-Write a short summary file for this read set.
-
-writeTexSummary(int, PrintWriter) References
-Write reference summary to LaTeX report.
-
-
-
A B C D E F G I K L M N O P R S T V W B-Index
-
-JavaScript is disabled on your browser.
-
-
-
-
-
-A B C D E F G I K L M N O P R S T V W
-
-
-
B
-
-BLASRParser nanook
-Parser for BLASR files
-
-BLASRParser(NanoOKOptions, References) BLASRParser
-BWAParser nanook
-Parser for BWA files
-
-BWAParser(NanoOKOptions, References) BWAParser
-
-
A B C D E F G I K L M N O P R S T V W C-Index
-
-JavaScript is disabled on your browser.
-
-
-
-
-
-A B C D E F G I K L M N O P R S T V W
-
-
-
C
-
-calculateBottomBaseCounts() KmerMotifStatistic
-Update motif bases counts for bottom 10 motifs
-
-calculateMotifs() KmerMotifStatistic
-Calculate percent each motif has been seen.
-
-calculateStats() ReadSetStats
-Calculate various statistics, e.g.
-
-calculateTopBaseCounts() KmerMotifStatistic
-Update motif base counts for top 10 motifs
-
-checkAndMakeReferenceAnalysisDir(String) NanoOKOptions
-Check if an analysis reference directory exists and make if not.
-
-checkCommand(String) ProcessLogger
-checkDependencies() NanoOK
-Check for program dependencies - R, pdflatex
-
-checkDirectoryStructure() NanoOKOptions
-Check if various required directories exist and create if not.
-
-CIGARString nanook
-Represent and parse a CIGAR string
-
-CIGARString(String, String, String, String, int, String, ReferenceSequence) CIGARString
-Constructor
-
-clearStats() ReferenceSequenceStats
-Clear all stats.
-
-close() NanoOKLog
-close() ReadLengthsSummaryFile
-Close output file.
-
-close() ReportWriter
-Close the .tex file.
-
-closeFile() GCCounter
-Close file
-
-closeKmersFile() ReadSetStats
-closeLengthsFile() ReadSetStats
-Close the read lengths file.
-
-compareTo(Object) Alignment
-compareTo(Object) KmerAbundance
-compareTo(Object) ReferenceSequence
-countKmer(String) KmerTable
-createDirectories() ReadAligner
-Create directories for output
-
-createDirectories() ReadExtractor
-Create directories for output
-
-
-
A B C D E F G I K L M N O P R S T V W D-Index
-
-JavaScript is disabled on your browser.
-
-
-
-
-
-A B C D E F G I K L M N O P R S T V W
-
-
-
D
-
-doKmerCounting() NanoOKOptions
-doMakePDF() NanoOKOptions
-Check if to make report or not
-
-doMakeReport() NanoOKOptions
-Check if to make report or not
-
-doParseAlignments() NanoOKOptions
-Check if to parse alignments or not
-
-doPlotGraphs() NanoOKOptions
-Check if to plot graphs or not
-
-drawImage() SequenceLogo
-Draw the logo image.
-
-
-
A B C D E F G I K L M N O P R S T V W E-Index
-
-JavaScript is disabled on your browser.
-
-
-
-
-
-A B C D E F G I K L M N O P R S T V W
-
-
-
E
-
-endMergeAndStoreStats() AlignmentMerger
-Declare end of alignment merge
-
-extract() ReadExtractor
-Extract reads
-
-
-
A B C D E F G I K L M N O P R S T V W F-Index
-
-JavaScript is disabled on your browser.
-
-
-
-
-
-A B C D E F G I K L M N O P R S T V W
-
-
-
F
-
-FASTA NanoOKOptions
-FASTQ NanoOKOptions
-filename ReadExtractorRunnable
-fixIDs() NanoOKOptions
-fixRandom() NanoOKOptions
-
-
A B C D E F G I K L M N O P R S T V W G-Index
-
-JavaScript is disabled on your browser.
-
-
-
-
-
-A B C D E F G I K L M N O P R S T V W
-
-
-
G
-
-GCCounter nanook
-Count GC content in references
-
-GCCounter(int, String) GCCounter
-get(String) KmerTable
-getAlignedNegativeStrandPercent() ReferenceSequenceStats
-Get percent of reads aligned on -ve strand
-
-getAlignedPercentIdentical() ReferenceSequenceStats
-Get percent identity of aligned bases.
-
-getAlignedPercentIdenticalWithoutIndels() ReferenceSequenceStats
-Get percent identity of aligned bases.
-
-getAlignedPositiveStrandPercent() ReferenceSequenceStats
-Get percent of reads aligned on +ve strand
-
-getAligner() NanoOKOptions
-getAlignerDir() NanoOKOptions
-Get LAST directory.
-
-getAlignerParams() NanoOKOptions
-getAlignment() MAFAlignmentLine
-Get alignment string.
-
-getAlignmentFileExtension() AlignmentFileParser
-Get file extension of alignments
-
-getAlignmentFileExtension() MAFParser
-Get file extension of alignment files
-
-getAlignmentFileExtension() SAMParser
-Get file extension of alignment files
-
-getAlignmentId() AlignmentInfo
-Get alignment identity.
-
-getAlignmentIdMinusIndels() AlignmentInfo
-Get alignment identity.
-
-getAlignmentSize() AlignmentInfo
-Get alignment size.
-
-getAlignmentSize() AlignmentMerger
-Get size of alignment without indels
-
-getAlignmentsTableFile() ReferenceSequenceStats
-Get the associated AlignmentsTableFile object
-
-getAlignmentSummaryFilename() NanoOKOptions
-Get filename of alignment summary file.
-
-getAllIds() References
-Return set of all reference sequence IDs.
-
-getAlnSize() MAFAlignmentLine
-Get alignment size.
-
-getAnalysisDir() NanoOKOptions
-Get analysis directory.
-
-getBinSize() ReferenceSequence
-Get bin size for graph plotting
-
-getCommandOutput(String, boolean, boolean) ProcessLogger
-getCoverageBinSize() NanoOKOptions
-Get coverage graph bin size.
-
-getDifference() KmerAbundance
-getEnd() MAFAlignmentLine
-Get end position of alignment
-
-getErrorTypeFromInt(int) NanoOKOptions
-Get an error type string (Insertion, Deletion, Substitution) from an integer.
-
-getFast5Dir() NanoOKOptions
-getFastaDir() NanoOKOptions
-getFastqDir() NanoOKOptions
-getGraphsDir() NanoOKOptions
-Get graphs directory.
-
-getHighestScoringSet() AlignmentFileParser
-Get highest scoring set of alignments (ie.
-
-getHighestScoringSet() MAFParser
-Get the set of alignments that match the highest scoring reference
-
-getHighestScoringSet() SAMParser
-Get the set of alignments that match the highest scoring reference
-
-getHitAlignmentSize() Alignment
-getHitAlnSize() CIGARString
-getHitEnd() Alignment
-getHitName() Alignment
-getHitName() AlignmentInfo
-getHitSequenceSize() Alignment
-getHitSize() AlignmentInfo
-Get hit size.
-
-getHitStart() Alignment
-getHitStrand() Alignment
-getHitString() Alignment
-getHitString() CIGARString
-getId() ReferenceSequence
-Get ID for this sequence.
-
-getID(int) SequenceReader
-getIdenticalBases() AlignmentInfo
-Get identical bases count.
-
-getkCounts() AlignmentInfo
-getKeys() KmerTable
-getKmer() KmerAbundance
-getKmerAbundance() ReferenceSequenceStats
-getKmerSize() KmerTable
-getKmerTable() ReferenceSequence
-Get kmer table
-
-getLatexDir() NanoOKOptions
-Get LaTeX directory.
-
-getLength(int) SequenceReader
-getLengthSummaryFilename() NanoOKOptions
-Get filename of length summary file.
-
-getLog() NanoOKOptions
-getLogsDir() NanoOKOptions
-Get logs directory.
-
-getLongest() ReadSetStats
-Get longest read in this read set.
-
-getLongestIdLength() References
-Get the length of the longest ID - used for formatting output.
-
-getLongestPerfectKmer() AlignmentInfo
-Get longest perfect kmer.
-
-getLongestPerfectKmer() ReferenceSequenceStats
-Get longest perfect kmer length.
-
-getMaxReads() NanoOKOptions
-Get maximum number of reads (used for debugging)
-
-getMeanDeletionSize() ReferenceSequenceStats
-Get the mean deletion size
-
-getMeanInsertionSize() ReferenceSequenceStats
-Get the mean insertion size
-
-getMeanLength() ReadSetStats
-Get mean length of reads in this read set.
-
-getMeanPerfectKmer() AlignmentInfo
-Get mean perfect kmer size.
-
-getMeanReadLength() ReferenceSequenceStats
-Get mean read length
-
-getMotifStatistics() ReadSetStats
-Get motif statistics.
-
-getN50() ReadSetStats
-Get N50 for this read set.
-
-getN50Count() ReadSetStats
-Get N50 count - number of reads of length N50 or greater.
-
-getN90() ReadSetStats
-Get N90 for this read set.
-
-getN90Count() ReadSetStats
-Get N90 count - number of reads of length N90 or greater.
-
-getName() MAFAlignmentLine
-Get name (ID) of sequence.
-
-getName() ReferenceSequence
-Get display name for this sequence.
-
-getNumberOfDeletionErrors() ReferenceSequenceStats
-Get number of deletion errors.
-
-getNumberOfFailFiles() ReadSetStats
-Get number of read files in fail directory
-
-getNumberOfInsertionErrors() ReferenceSequenceStats
-Getnumber of insertion errors.
-
-getNumberOfPassFiles() ReadSetStats
-Get number of read files in pass directory
-
-getNumberOfReads() ReadSetStats
-Get number of reads in this read set.
-
-getNumberOfReadsWithAlignments() ReadSetStats
-Get number of reads with alignments in this read set.
-
-getNumberOfReadsWithAlignments() ReferenceSequenceStats
-Get number of reads with alignments.
-
-getNumberOfReadsWithoutAlignments() ReadSetStats
-Get number of reads without alignments in this read set.
-
-getNumberOfReferences() References
-Get number of references.
-
-getNumberOfSubstitutionErrors() ReferenceSequenceStats
-Get number of substitution errors.
-
-getNumberOfSubstitutions() ReadSetStats
-Get number of substitutions.
-
-getNumberOfThreads() NanoOKOptions
-getNumberOfTypes() NanoOKOptions
-getNumReadFiles() ReadSetStats
-Get number of read files.
-
-getNumReads() ReadSetStats
-Get number of reads.
-
-getOverallHitEnd() AlignmentMerger
-Get hit end position of merged alignment
-
-getOverallHitSize() AlignmentMerger
-Get size of hit covered by merged alignment
-
-getOverallHitStart() AlignmentMerger
-Get hit start position of merged alignment
-
-getOverallQueryEnd() AlignmentMerger
-Get query end position of merged alignment
-
-getOverallQuerySize() AlignmentMerger
-Get size of query covered by merged alignment
-
-getOverallQueryStart() AlignmentMerger
-Get query start position of merged alignment
-
-getParser() NanoOKOptions
-Get the right parser
-
-getPercentDeletionErrors() ReferenceSequenceStats
-Get percentage of deletion errors
-
-getPercentInsertionErrors() ReferenceSequenceStats
-Get percentage of insertion errors
-
-getPercentOfReadsWithAlignments() ReadSetStats
-Get percentage of reads with alignments
-
-getPercentOfReadsWithoutAlignments() ReadSetStats
-Get percentage of reads without alignments
-
-getPercentQueryAligned() AlignmentInfo
-Get percentage of query aligned.
-
-getPercentSubstitutionErrors() ReferenceSequenceStats
-Get percentage of substitution errors
-
-getPrintWriter() NanoOKLog
-getPrintWriter() ReportWriter
-Get handle to PrintWriter.
-
-getProgramID() AlignmentFileParser
-Get identifier for the alignment program
-
-getProgramID() BLASRParser
-getProgramID() BWAParser
-getProgramID() LastParser
-getProgramID() MarginAlignParser
-getQuertEnd() Alignment
-getQueryAlignmentSize() Alignment
-getQueryAlnSize() CIGARString
-getQueryId() AlignmentInfo
-Get query identity.
-
-getQueryName() Alignment
-getQueryName() AlignmentInfo
-getQuerySequenceSize() Alignment
-getQuerySize() AlignmentInfo
-Get query size.
-
-getQueryStart() Alignment
-getQueryStart() CIGARString
-getQueryStrand() Alignment
-getQueryString() Alignment
-getQueryString() CIGARString
-getQueue() NanoOKOptions
-getReadAbundance() KmerAbundance
-getReadDir() NanoOKOptions
-Get FASTA directory.
-
-getReadFormat() AlignmentFileParser
-Get format of input reads expected
-
-getReadFormat() BLASRParser
-getReadFormat() BWAParser
-getReadFormat() LastParser
-getReadFormat() MarginAlignParser
-getReadFormat() NanoOKOptions
-getReadKmerTable() ReferenceSequenceStats
-getReadLength(String) ReadSetStats
-Get length of read
-
-getReadPercentIdentical() ReferenceSequenceStats
-Get percent identity of read.
-
-getRefAbundance() KmerAbundance
-getReferenceById(String) References
-Get a ReferenceSequence object from sequence ID.
-
-getReferenceFile() NanoOKOptions
-Get name of references file.
-
-getReferences() NanoOKOptions
-getRunCommand(String, String, String) AlignmentFileParser
-Get command to run aligner
-
-getRunCommand(String, String, String) BLASRParser
-getRunCommand(String, String, String) BWAParser
-getRunCommand(String, String, String) LastParser
-getRunCommand(String, String, String) MarginAlignParser
-getRunMode() NanoOKOptions
-getSample() NanoOKOptions
-Get sample name.
-
-getSampleDirectory() NanoOKOptions
-getScheduler() NanoOKOptions
-getScore() Alignment
-getScriptsDir() NanoOKOptions
-Get scripts directory.
-
-getSeqSize() MAFAlignmentLine
-Get sequence size.
-
-getSequenceCount() SequenceReader
-getShortest() ReadSetStats
-Get shortest read in this read set.
-
-getSize() ReferenceSequence
-Get size (length) of this sequence.
-
-getSortedDeletionMotifCounts(int) MotifStatistics
-Get a sorted list of deletion motif counts at given kmer size.
-
-getSortedDeletionMotifPercentages(int) MotifStatistics
-Get a sorted list of deletion motif percentages at given kmer size.
-
-getSortedInsertionMotifCounts(int) MotifStatistics
-Get a sorted list of insertion motif counts at given kmer size.
-
-getSortedInsertionMotifPercentages(int) MotifStatistics
-Get a sorted list of insertion motif percentages at given kmer size.
-
-getSortedMotifCounts() KmerMotifStatistic
-Return ArrayList of sorted motif counts.
-
-getSortedMotifPercentages() KmerMotifStatistic
-Return ArrayList of sorted motif percentages.
-
-getSortedReferences() References
-Return sorted set of all reference sequence IDs.
-
-getSortedSubstitutionMotifCounts(int) MotifStatistics
-Get a sorted list of substitution motif counts at given kmer size.
-
-getSortedSubstitutionMotifPercentages(int) MotifStatistics
-Get a sorted list of substitution motif percentages at given kmer size.
-
-getStart() MAFAlignmentLine
-Get start position of alignment.
-
-getStats() ReadSet
-Get stats object.
-
-getStatsByType(int) OverallStats
-Get a set of stats (for either Template, Complement or 2D reads)
-
-getStatsByType(int) ReferenceSequence
-Get stats for a particular type (Template, Complement, 2D).
-
-getStrand() MAFAlignmentLine
-Get strand.
-
-getSubSequence(String, int, int) SequenceReader
-getSubstitutionErrors() ReadSetStats
-Get substitution error matrix (A, C, G, T vs A, C, G, T).
-
-getTable() KmerTable
-getTexFilename() NanoOKOptions
-Get LaTeX filename.
-
-getTotalAlignedBases() ReferenceSequenceStats
-Get the number of aligned bases
-
-getTotalBases() ReadSetStats
-Get total bases represented by read set.
-
-getTotalMotifCount() KmerMotifStatistic
-Get total motif count.
-
-getTotalMotifCounts(int, int) MotifStatistics
-Get total count of motifs seen
-
-getType() ReadSetStats
-Get type
-
-getTypeFromInt(int) NanoOKOptions
-Get a type string (Template, Complement, 2D) from an integer.
-
-getTypeString() ReadSet
-Get type of this read set.
-
-getTypeString() ReadSetStats
-Get type as a string.
-
-
-
A B C D E F G I K L M N O P R S T V W I-Index
-
-JavaScript is disabled on your browser.
-
-
-
-
-
-A B C D E F G I K L M N O P R S T V W
-
-
-
I
-
-indexFASTAFile(String, String, boolean) SequenceReader
-Parse a FASTA file
-
-indexFASTQFile(String) SequenceReader
-inDir ReadExtractorRunnable
-initialiseAlignmentSummaryFile() NanoOKOptions
-Create a new alignment summary file.
-
-isCIGAR() Alignment
-isNewStyleDir() NanoOKOptions
-isProcessing2DReads() NanoOKOptions
-isProcessingComplementReads() NanoOKOptions
-isProcessingFailReads() NanoOKOptions
-Check if processing "fail" reads.
-
-isProcessingPassReads() NanoOKOptions
-Check if processing "pass" reads.
-
-isProcessingReadType(int) NanoOKOptions
-isProcessingTemplateReads() NanoOKOptions
-isValidReadFile(String) ReadAligner
-
-
A B C D E F G I K L M N O P R S T V W K-Index
-
-JavaScript is disabled on your browser.
-
-
-
-
-
-A B C D E F G I K L M N O P R S T V W
-
-
-
K
-
-KmerAbundance nanook
-Represent abundance of a kmer
-
-KmerAbundance(String, double, double) KmerAbundance
-KmerMotifStatistic nanook
-Class to store kmer motif statistics.
-
-KmerMotifStatistic(int) KmerMotifStatistic
-Constructor
-
-KmerTable nanook
-KmerTable used for 5-mer comparison
-
-KmerTable(int) KmerTable
-
-
A B C D E F G I K L M N O P R S T V W Generated Documentation (Untitled)
-
-
-
-<![CDATA[
-<noscript>
-<div>JavaScript is disabled on your browser.</div>
-</noscript>
-<h2>Frame Alert</h2>
-<p>This document is designed to be viewed using the frames feature. If you see this message, you are using a non-frame-capable web client. Link to <a href="nanook/package-summary.html">Non-frame version</a>.</p>
-]]>
-
-
diff --git a/dist/javadoc/nanook/Alignment.html b/dist/javadoc/nanook/Alignment.html
deleted file mode 100644
index 58f52a5..0000000
--- a/dist/javadoc/nanook/Alignment.html
+++ /dev/null
@@ -1,534 +0,0 @@
-
-
-
-
-
-Alignment
-
-JavaScript is disabled on your browser.
-
-
-
-
-
-
-
-
-
-java.lang.Object
-
-
-
-
-
-
-
-
-
-
-
-
-
-Constructor Summary
-
-Constructors
-Constructor and Description
-
-
-Alignment
-
-
-
-
-
-
-
-Method Summary
-
-
-
-
-
-Methods inherited from class java.lang.Object
-clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
-
-
-
-
-
-
-
-
-
-
-
-
-Constructor Detail
-
-
-
-
-
-Alignment
-public Alignment(int s,
- java.lang.String qName,
- int qSize,
- int qStart,
- int qAlnSize,
- java.lang.String qs,
- java.lang.String hName,
- int hSize,
- int hStart,
- int hAlnSize,
- java.lang.String hs,
- boolean cigar)
-
-
-
-
-
-
-
-
-Method Detail
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-getScore
-public int getScore()
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-getQuertEnd
-public int getQuertEnd()
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-getHitStart
-public int getHitStart()
-
-
-
-
-
-
-
-
-
-
-
-getHitEnd
-public int getHitEnd()
-
-
-
-
-
-
-
-
-
-
-
-isCIGAR
-public boolean isCIGAR()
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
AlignmentFileParser
-
-JavaScript is disabled on your browser.
-
-
-
-
-
-
-
-
-
-
-
-
-Summary:
-Nested |
-Field |
-Constr |
-Method
-
-Detail:
-Field |
-Constr |
-Method
-
-
-
-
-
-
-
-
-
-
-
-
-
-Method Summary
-
-Methods
-Modifier and Type
-Method and Description
-
-
-java.lang.StringgetAlignmentFileExtension Get file extension of alignments
-
-
-java.util.List<Alignment >getHighestScoringSet Get highest scoring set of alignments (ie.
-
-
-java.lang.StringgetProgramID Get identifier for the alignment program
-
-
-intgetReadFormat Get format of input reads expected
-
-
-java.lang.StringgetRunCommand Get command to run aligner
-
-
-booleanoutputsToStdout Return true if this aligner outputs to Stdout and not a file
-
-
-intparseFile AlignmentsTableFile summaryFile,
- ReadSetStats overallStats)Parse an alignment file.
-
-
-voidsetAlignmentParams Set alignment parameters to run executable
-
-
-voidsortAlignments Sort alignments by score
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-Method Detail
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-getRunCommand
-java.lang.String getRunCommand(java.lang.String query,
- java.lang.String output,
- java.lang.String reference)
-Get command to run aligner
-Parameters: query - query fileoutput - output filereference - reference fileReturns:
-
-
-
-
-
-
-
-
-
-
-sortAlignments
-void sortAlignments()
-Sort alignments by score
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-Summary:
-Nested |
-Field |
-Constr |
-Method
-
-Detail:
-Field |
-Constr |
-Method
-
-
-
- AlignmentInfo
-
-JavaScript is disabled on your browser.
-
-
-
-
-
-
-
-
-
-java.lang.Object
-
-
-
-
-
-
-
-
-
-
-
-
-
-Constructor Summary
-
-Constructors
-Constructor and Description
-
-
-AlignmentInfo Constructor.
-
-
-
-
-
-
-
-
-Method Summary
-
-
-
-
-
-Methods inherited from class java.lang.Object
-clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
-
-
-
-
-
-
-
-
-
-
-
-
-Constructor Detail
-
-
-
-
-
-AlignmentInfo
-public AlignmentInfo(java.lang.String hn,
- int hs,
- java.lang.String qn,
- int qs,
- int ib,
- int l,
- int t,
- int c,
- int as,
- int ami,
- int qas)
-Constructor.
-Parameters: hn - hit namehs - hit sizeqn - query nameqs - query sizeib - number of identical basesl - longest perfect kmert - sum of perfect kmersc - count of perfect kmersas - alignment sizead - alignment size minus indelsqas - query alignment size
-
-
-
-
-
-
-
-Method Detail
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-getHitSize
-public int getHitSize()
-Get hit size.
-Returns: size of hit, in bases
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
AlignmentMerger
-
-JavaScript is disabled on your browser.
-
-
-
-
-
-
-
-
-
-java.lang.Object
-
-
-nanook.AlignmentMerger
-
-
-
-
-
-
-
-
-
-
-
-
-Constructor Summary
-
-
-
-
-
-
-
-Method Summary
-
-
-
-
-
-Methods inherited from class java.lang.Object
-clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
-
-
-
-
-
-
-
-
-
-
-
-
-Constructor Detail
-
-
-
-
-
-AlignmentMerger
-public AlignmentMerger(NanoOKOptions o,
- ReferenceSequence r,
- int l,
- ReadSetStats s,
- int t)
-Constructor
-Parameters: r - the reference, as a ReferenceSequence objectl - the read lengths - the read set stats for this read sett - the type number of read (defined in NanoOKOptions)
-
-
-
-
-
-
-
-
AlignmentsTableFile
-
-JavaScript is disabled on your browser.
-
-
-
-
-
-
-
-
-
-java.lang.Object
-
-
-nanook.AlignmentsTableFile
-
-
-
-
-
-
-
-
-
-
-
-
-Constructor Summary
-
-Constructors
-Constructor and Description
-
-
-AlignmentsTableFile Constructor.
-
-
-
-
-
-
-
-
-Method Summary
-
-
-
-
-
-Methods inherited from class java.lang.Object
-clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
-
-
-
-
-
-
-
-
-
-
-
-
-Constructor Detail
-
-
-
-
-
-
-
-
-
-
-Method Detail
-
-
-
-
-
-writeAlignment
-public void writeAlignment(java.lang.String alignmentFilename,
- MAFAlignmentLine hitLine,
- MAFAlignmentLine queryLine,
- AlignmentInfo stat)
-Write an alignment line.
-Parameters: alignmentFilename - filename of alignmenthitLine - hit objectqueryLine - query objectstat - AlignmentInfo statistics
-
-
-
-
-
-
-
-
-
-
-
-
-
-
BLASRParser
-
-JavaScript is disabled on your browser.
-
-
-
-
-
-
-
-
-
-java.lang.Object
-
-
-
-
-
-
-
-
-
-
-
-
-
-Constructor Summary
-
-
-
-
-
-
-
-Method Summary
-
-Methods
-Modifier and Type
-Method and Description
-
-
-java.lang.StringgetProgramID Get identifier for the alignment program
-
-
-intgetReadFormat Get format of input reads expected
-
-
-java.lang.StringgetRunCommand Get command to run aligner
-
-
-booleanoutputsToStdout Return true if this aligner outputs to Stdout and not a file
-
-
-voidsetAlignmentParams Set alignment parameters to run executable
-
-
-
-
-
-
-
-Methods inherited from class java.lang.Object
-clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
-
-
-
-
-
-
-
-
-
-
-
-
-
-Constructor Detail
-
-
-
-
-
-
-
-
-
-
-Method Detail
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-getRunCommand
-public java.lang.String getRunCommand(java.lang.String query,
- java.lang.String output,
- java.lang.String reference)
-
-Get command to run aligner
-
-Specified by: getRunCommand AlignmentFileParser Parameters: query - query fileoutput - output filereference - reference fileReturns:
-
-
-
-
-
-
-
-
-
-
-
BWAParser
-
-JavaScript is disabled on your browser.
-
-
-
-
-
-
-
-
-
-java.lang.Object
-
-
-
-
-
-
-
-
-
-
-
-
-
-Constructor Summary
-
-
-
-
-
-
-
-Method Summary
-
-Methods
-Modifier and Type
-Method and Description
-
-
-java.lang.StringgetProgramID Get identifier for the alignment program
-
-
-intgetReadFormat Get format of input reads expected
-
-
-java.lang.StringgetRunCommand Get command to run aligner
-
-
-booleanoutputsToStdout Return true if this aligner outputs to Stdout and not a file
-
-
-voidsetAlignmentParams Set alignment parameters to run executable
-
-
-
-
-
-
-
-Methods inherited from class java.lang.Object
-clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
-
-
-
-
-
-
-
-
-
-
-
-
-
-Constructor Detail
-
-
-
-
-
-
-
-
-
-
-Method Detail
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-getRunCommand
-public java.lang.String getRunCommand(java.lang.String query,
- java.lang.String output,
- java.lang.String reference)
-
-Get command to run aligner
-
-Specified by: getRunCommand AlignmentFileParser Parameters: query - query fileoutput - output filereference - reference fileReturns:
-
-
-
-
-
-
-
CIGARString
-
-JavaScript is disabled on your browser.
-
-
-
-
-
-
-
-
-
-java.lang.Object
-
-
-
-
-
-
-
-
-
-
-
-
-
-Constructor Summary
-
-Constructors
-Constructor and Description
-
-
-CIGARString ReferenceSequence hr)Constructor
-
-
-
-
-
-
-
-
-Method Summary
-
-
-
-
-
-Methods inherited from class java.lang.Object
-clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
-
-
-
-
-
-
-
-
-
-
-
-
-Constructor Detail
-
-
-
-
-
-CIGARString
-public CIGARString(java.lang.String cs,
- java.lang.String qseq,
- java.lang.String qf,
- java.lang.String qi,
- int hs,
- java.lang.String hf,
- ReferenceSequence hr)
-Constructor
-Parameters: cs - qseq - qf - hs - hit start position (0-based)hf - hr -
-
-
-
-
-
-
-
-
GCCounter
-
-JavaScript is disabled on your browser.
-
-
-
-
-
-
-
-
-
-java.lang.Object
-
-
-
-
-
-
-
-
-
-
-
-
-
-Constructor Summary
-
-Constructors
-Constructor and Description
-
-
-GCCounter
-
-
-
-
-
-
-
-Method Summary
-
-Methods
-Modifier and Type
-Method and Description
-
-
-voidaddString Process sequence string
-
-
-voidcloseFile Close file
-
-
-
-
-
-
-Methods inherited from class java.lang.Object
-clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
-
-
-
-
-
-
-
-
-
-
-
-
-Constructor Detail
-
-
-
-
-
-
-
-
-
-
-Method Detail
-
-
-
-
-
-closeFile
-public void closeFile()
-Close file
-
-
-
-
-
-
-
-
-
-
-
KmerAbundance
-
-JavaScript is disabled on your browser.
-
-
-
-
-
-
-
-
-
-java.lang.Object
-
-
-
-
-
-
-
-
-
-
-
-
-
-Constructor Summary
-
-Constructors
-Constructor and Description
-
-
-KmerAbundance
-
-
-
-
-
-
-
-Method Summary
-
-
-
-
-
-Methods inherited from class java.lang.Object
-clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
-
-
-
-
-
-
-
-
-
-
-
-
-Constructor Detail
-
-
-
-
-
-
-
-
-
-
-
KmerMotifStatistic
-
-JavaScript is disabled on your browser.
-
-
-
-
-
-
-
-
-
-java.lang.Object
-
-
-nanook.KmerMotifStatistic
-
-
-
-
-
-
-
-
-
-
-
-
-Field Summary
-
-Fields
-Modifier and Type
-Field and Description
-
-
-static intTYPE_BOTTOM
-
-static intTYPE_TOP
-
-
-
-
-
-
-
-Constructor Summary
-
-Constructors
-Constructor and Description
-
-
-KmerMotifStatistic Constructor
-
-
-
-
-
-
-
-
-Method Summary
-
-Methods
-Modifier and Type
-Method and Description
-
-
-voidaddMotif Add a motif to store.
-
-
-voidcalculateBottomBaseCounts Update motif bases counts for bottom 10 motifs
-
-
-voidcalculateMotifs Calculate percent each motif has been seen.
-
-
-voidcalculateTopBaseCounts Update motif base counts for top 10 motifs
-
-
-java.util.ArrayList<java.util.Map.Entry<java.lang.String,java.lang.Integer>>getSortedMotifCounts Return ArrayList of sorted motif counts.
-
-
-java.util.ArrayList<java.util.Map.Entry<java.lang.String,java.lang.Double>>getSortedMotifPercentages Return ArrayList of sorted motif percentages.
-
-
-intgetTotalMotifCount Get total motif count.
-
-
-voidoutputMotifCounts Write motif counts to stdout.
-
-
-voidwriteLogoImage Write a top 10 or bottom 10 logo image.
-
-
-
-
-
-
-Methods inherited from class java.lang.Object
-clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-Constructor Detail
-
-
-
-
-
-
-
-
-
-
-Method Detail
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-writeLogoImage
-public void writeLogoImage(int type,
- java.lang.String filename)
-Write a top 10 or bottom 10 logo image.
-Parameters: type - TYPE_TOP for Top 10 or TYPE_BOTTOM for bottom 10filename - PNG output filename
-
-
-
-
-
-
-getSortedMotifCounts
-public java.util.ArrayList<java.util.Map.Entry<java.lang.String,java.lang.Integer>> getSortedMotifCounts()
-Return ArrayList of sorted motif counts.
-Returns: sorted motifs
-
-
-
-
-
-
-getSortedMotifPercentages
-public java.util.ArrayList<java.util.Map.Entry<java.lang.String,java.lang.Double>> getSortedMotifPercentages()
-Return ArrayList of sorted motif percentages.
-Returns: sorted motifs
-
-
-
-
-
-
-
-
-
-
-
-
-
-
KmerTable
-
-JavaScript is disabled on your browser.
-
-
-
-
-
-
-
-
-
-java.lang.Object
-
-
-
-
-
-
-
-
-
-
-
-
-
-Constructor Summary
-
-Constructors
-Constructor and Description
-
-
-KmerTable
-
-
-
-
-
-
-
-Method Summary
-
-Methods
-Modifier and Type
-Method and Description
-
-
-voidcountKmer
-
-intget
-
-java.util.Set<java.lang.String>getKeys
-
-intgetKmerSize
-
-java.util.HashtablegetTable
-
-voidwriteKmerTable
-
-
-
-
-
-Methods inherited from class java.lang.Object
-clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
-
-
-
-
-
-
-
-
-
-
-
-
-Constructor Detail
-
-
-
-
-
-KmerTable
-public KmerTable(int k)
-
-
-
-
-
-
-
-
-Method Detail
-
-
-
-
-
-
-
-
-
-
-
-
-
-getKmerSize
-public int getKmerSize()
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
LastParser
-
-JavaScript is disabled on your browser.
-
-
-
-
-
-
-
-
-
-java.lang.Object
-
-
-
-
-
-
-
-
-
-
-
-
-
-Constructor Summary
-
-
-
-
-
-
-
-Method Summary
-
-Methods
-Modifier and Type
-Method and Description
-
-
-java.lang.StringgetProgramID Get identifier for the alignment program
-
-
-intgetReadFormat Get format of input reads expected
-
-
-java.lang.StringgetRunCommand Get command to run aligner
-
-
-booleanoutputsToStdout Return true if this aligner outputs to Stdout and not a file
-
-
-voidsetAlignmentParams Set alignment parameters to run executable
-
-
-
-
-
-
-
-Methods inherited from class java.lang.Object
-clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
-
-
-
-
-
-
-
-
-
-
-
-
-
-Constructor Detail
-
-
-
-
-
-
-
-
-
-
-Method Detail
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-getRunCommand
-public java.lang.String getRunCommand(java.lang.String query,
- java.lang.String output,
- java.lang.String reference)
-
-Get command to run aligner
-
-Specified by: getRunCommand AlignmentFileParser Parameters: query - query fileoutput - output filereference - reference fileReturns:
-
-
-
-
-
-
-
-
-
-
-
MAFAlignmentLine
-
-JavaScript is disabled on your browser.
-
-
-
-
-
-
-
-
-
-java.lang.Object
-
-
-nanook.MAFAlignmentLine
-
-
-
-
-
-
-
-
-
-
-
-
-Constructor Summary
-
-Constructors
-Constructor and Description
-
-
-MAFAlignmentLine Constructor.
-
-
-
-
-
-
-
-
-Method Summary
-
-Methods
-Modifier and Type
-Method and Description
-
-
-java.lang.StringgetAlignment Get alignment string.
-
-
-intgetAlnSize Get alignment size.
-
-
-intgetEnd Get end position of alignment
-
-
-java.lang.StringgetName Get name (ID) of sequence.
-
-
-intgetSeqSize Get sequence size.
-
-
-intgetStart Get start position of alignment.
-
-
-java.lang.StringgetStrand Get strand.
-
-
-
-
-
-
-Methods inherited from class java.lang.Object
-clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
-
-
-
-
-
-
-
-
-
-
-
-
-Constructor Detail
-
-
-
-
-
-
-
-
-
-
-Method Detail
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-getAlnSize
-public int getAlnSize()
-Get alignment size.
-Returns: alignment size, in bases
-
-
-
-
-
-
-
-
-
-
-getSeqSize
-public int getSeqSize()
-Get sequence size.
-Returns: sequence size, in bases.
-
-
-
-
-
-
-
-
-
-
MAFParser
-
-JavaScript is disabled on your browser.
-
-
-
-
-
-
-
-
-
-java.lang.Object
-
-
-
-
-
-
-
-
-
-
-
-
-
-Constructor Summary
-
-
-
-
-
-
-
-Method Summary
-
-
-
-
-
-Methods inherited from class java.lang.Object
-clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
-
-
-
-
-
-
-
-
-
-
-
-
-Constructor Detail
-
-
-
-
-
-
-
-
-
-
-
MarginAlignParser
-
-JavaScript is disabled on your browser.
-
-
-
-
-
-
-
-
-
-java.lang.Object
-
-
-
-
-
-
-
-
-
-
-
-
-
-Constructor Summary
-
-
-
-
-
-
-
-Method Summary
-
-Methods
-Modifier and Type
-Method and Description
-
-
-java.lang.StringgetProgramID Get identifier for the alignment program
-
-
-intgetReadFormat Get format of input reads expected
-
-
-java.lang.StringgetRunCommand Get command to run aligner
-
-
-booleanoutputsToStdout Return true if this aligner outputs to Stdout and not a file
-
-
-voidsetAlignmentParams Set alignment parameters to run executable
-
-
-
-
-
-
-
-Methods inherited from class java.lang.Object
-clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
-
-
-
-
-
-
-
-
-
-
-
-
-
-Constructor Detail
-
-
-
-
-
-
-
-
-
-
-Method Detail
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-getRunCommand
-public java.lang.String getRunCommand(java.lang.String query,
- java.lang.String output,
- java.lang.String reference)
-
-Get command to run aligner
-
-Specified by: getRunCommand AlignmentFileParser Parameters: query - query fileoutput - output filereference - reference fileReturns:
-
-
-
-
-
-
-
-
-
-
-
MotifStatistics
-
-JavaScript is disabled on your browser.
-
-
-
-
-
-
-
-
-
-java.lang.Object
-
-
-nanook.MotifStatistics
-
-
-
-
-
-
-public class MotifStatistics
-extends java.lang.Object
-Store all motif statistics (ie, insertion, deletion, substitution) at a range
- of sizes (3, 4, 5) for a single read type (Template, Complement or 2D).
-
-
-
-
-
-
-
-
-
-
-
-Constructor Summary
-
-Constructors
-Constructor and Description
-
-
-MotifStatistics Constructor
-
-
-
-
-
-
-
-
-Method Summary
-
-Methods
-Modifier and Type
-Method and Description
-
-
-voidaddDeletionMotifs Add a deletion motif.
-
-
-voidaddInsertionMotifs Add a insertion motif.
-
-
-voidaddMotifs KmerMotifStatistic [] motif,
- java.lang.String kmer)Given a stretch of perfect sequence, store motifs at all k size.
-
-
-voidaddSubstitutionMotifs Add a substitution motif
-
-
-java.util.ArrayList<java.util.Map.Entry<java.lang.String,java.lang.Integer>>getSortedDeletionMotifCounts Get a sorted list of deletion motif counts at given kmer size.
-
-
-java.util.ArrayList<java.util.Map.Entry<java.lang.String,java.lang.Double>>getSortedDeletionMotifPercentages Get a sorted list of deletion motif percentages at given kmer size.
-
-
-java.util.ArrayList<java.util.Map.Entry<java.lang.String,java.lang.Integer>>getSortedInsertionMotifCounts Get a sorted list of insertion motif counts at given kmer size.
-
-
-java.util.ArrayList<java.util.Map.Entry<java.lang.String,java.lang.Double>>getSortedInsertionMotifPercentages Get a sorted list of insertion motif percentages at given kmer size.
-
-
-java.util.ArrayList<java.util.Map.Entry<java.lang.String,java.lang.Integer>>getSortedSubstitutionMotifCounts Get a sorted list of substitution motif counts at given kmer size.
-
-
-java.util.ArrayList<java.util.Map.Entry<java.lang.String,java.lang.Double>>getSortedSubstitutionMotifPercentages Get a sorted list of substitution motif percentages at given kmer size.
-
-
-intgetTotalMotifCounts Get total count of motifs seen
-
-
-voidoutputAllMotifCounts Output motif counts for all types (debugging).
-
-
-voidwriteDeletionLogoImage Write deletion logo image (via KmerMotifStatistic object)
-
-
-voidwriteInsertionLogoImage Write insertion logo image (via KmerMotifStatistic object)
-
-
-voidwriteSubstitutionLogoImage Write substitution logo image (via KmerMotifStatistic object)
-
-
-
-
-
-
-Methods inherited from class java.lang.Object
-clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
-
-
-
-
-
-
-
-
-
-
-
-
-Constructor Detail
-
-
-
-
-
-MotifStatistics
-public MotifStatistics()
-Constructor
-
-
-
-
-
-
-
-
-Method Detail
-
-
-
-
-
-addMotifs
-public void addMotifs(KmerMotifStatistic [] motif,
- java.lang.String kmer)
-Given a stretch of perfect sequence, store motifs at all k size.
-Parameters: motif - KmerMotifStatistic object to add tokmer - perfect sequence to get motifs from
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-getSortedInsertionMotifCounts
-public java.util.ArrayList<java.util.Map.Entry<java.lang.String,java.lang.Integer>> getSortedInsertionMotifCounts(int k)
-Get a sorted list of insertion motif counts at given kmer size.
-Parameters: k - kmer size requiredReturns: ArrayList of counts.
-
-
-
-
-
-
-getSortedDeletionMotifCounts
-public java.util.ArrayList<java.util.Map.Entry<java.lang.String,java.lang.Integer>> getSortedDeletionMotifCounts(int k)
-Get a sorted list of deletion motif counts at given kmer size.
-Parameters: k - kmer size requiredReturns: ArrayList of counts.
-
-
-
-
-
-
-getSortedSubstitutionMotifCounts
-public java.util.ArrayList<java.util.Map.Entry<java.lang.String,java.lang.Integer>> getSortedSubstitutionMotifCounts(int k)
-Get a sorted list of substitution motif counts at given kmer size.
-Parameters: k - kmer size requiredReturns: ArrayList of counts.
-
-
-
-
-
-
-getSortedInsertionMotifPercentages
-public java.util.ArrayList<java.util.Map.Entry<java.lang.String,java.lang.Double>> getSortedInsertionMotifPercentages(int k)
-Get a sorted list of insertion motif percentages at given kmer size.
-Parameters: k - kmer size requiredReturns: ArrayList of counts.
-
-
-
-
-
-
-getSortedDeletionMotifPercentages
-public java.util.ArrayList<java.util.Map.Entry<java.lang.String,java.lang.Double>> getSortedDeletionMotifPercentages(int k)
-Get a sorted list of deletion motif percentages at given kmer size.
-Parameters: k - kmer size requiredReturns: ArrayList of counts.
-
-
-
-
-
-
-getSortedSubstitutionMotifPercentages
-public java.util.ArrayList<java.util.Map.Entry<java.lang.String,java.lang.Double>> getSortedSubstitutionMotifPercentages(int k)
-Get a sorted list of substitution motif percentages at given kmer size.
-Parameters: k - kmer size requiredReturns: ArrayList of counts.
-
-
-
-
-
-
-writeInsertionLogoImage
-public void writeInsertionLogoImage(int type,
- java.lang.String filename,
- int k)
-Write insertion logo image (via KmerMotifStatistic object)
-Parameters: type - either TYPE_TOP or TYPE_BOTTOM (Top 10 or bottom 10)filename - image filenamek - kmer size
-
-
-
-
-
-
-writeDeletionLogoImage
-public void writeDeletionLogoImage(int type,
- java.lang.String filename,
- int k)
-Write deletion logo image (via KmerMotifStatistic object)
-Parameters: type - either TYPE_TOP or TYPE_BOTTOM (Top 10 or bottom 10)filename - image filenamek - kmer size
-
-
-
-
-
-
-writeSubstitutionLogoImage
-public void writeSubstitutionLogoImage(int type,
- java.lang.String filename,
- int k)
-Write substitution logo image (via KmerMotifStatistic object)
-Parameters: type - either TYPE_TOP or TYPE_BOTTOM (Top 10 or bottom 10)filename - image filenamek - kmer size
-
-
-
-
-
-
-
-
-
-
NanoOK
-
-JavaScript is disabled on your browser.
-
-
-
-
-
-
-
-
-
-java.lang.Object
-
-
-
-
-
-
-
-
-
-
-
-
-
-Field Summary
-
-Fields
-Modifier and Type
-Field and Description
-
-
-static java.lang.StringVERSION_STRING
-
-
-
-
-
-
-
-Constructor Summary
-
-Constructors
-Constructor and Description
-
-
-NanoOK
-
-
-
-
-
-
-
-Method Summary
-
-
-
-
-
-Methods inherited from class java.lang.Object
-clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
-
-
-
-
-
-
-
-
-
-
-
-
-Field Detail
-
-
-
-
-
-
-
-
-
-
-Constructor Detail
-
-
-
-
-
-NanoOK
-public NanoOK()
-
-
-
-
-
-
-
-
-
NanoOKLog
-
-JavaScript is disabled on your browser.
-
-
-
-
-
-
-
-
-
-java.lang.Object
-
-
-
-
-
-
-
-
-
-
-
-
-
-Constructor Summary
-
-Constructors
-Constructor and Description
-
-
-NanoOKLog
-
-
-
-
-
-
-
-Method Summary
-
-Methods
-Modifier and Type
-Method and Description
-
-
-voidclose
-
-java.io.PrintWritergetPrintWriter
-
-voidopen
-
-voidprint
-
-voidprintln
-
-
-
-
-
-Methods inherited from class java.lang.Object
-clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
-
-
-
-
-
-
-
-
-
-
-
-
-Constructor Detail
-
-
-
-
-
-NanoOKLog
-public NanoOKLog()
-
-
-
-
-
-
-
-
-Method Detail
-
-
-
-
-
-
-
-
-
-close
-public void close()
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
NanoOKOptions
-
-JavaScript is disabled on your browser.
-
-
-
-
-
-
-
-
-
-java.lang.Object
-
-
-
-
-
-
-
-
-
-
-
-
-
-Field Summary
-
-
-
-
-
-
-
-Constructor Summary
-
-Constructors
-Constructor and Description
-
-
-NanoOKOptions
-
-
-
-
-
-
-
-Method Summary
-
-
-
-
-
-Methods inherited from class java.lang.Object
-clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-Constructor Detail
-
-
-
-
-
-NanoOKOptions
-public NanoOKOptions()
-
-
-
-
-
-
-
-
-Method Detail
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-getTypeFromInt
-public static java.lang.String getTypeFromInt(int n)
-Get a type string (Template, Complement, 2D) from an integer.
-Parameters: n - integer to convertReturns: type String
-
-
-
-
-
-
-getErrorTypeFromInt
-public static java.lang.String getErrorTypeFromInt(int n)
-Get an error type string (Insertion, Deletion, Substitution) from an integer.
-Parameters: n - error type integerReturns: type String
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-getRunMode
-public int getRunMode()
-
-
-
-
-
-
-
-fixIDs
-public boolean fixIDs()
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
OverallStats
-
-JavaScript is disabled on your browser.
-
-
-
-
-
-
-
-
-
-java.lang.Object
-
-
-
-
-
-
-
-public class OverallStats
-extends java.lang.Object
-Represents overall (as opposed to per reference) stats for Template, Complement and 2D reads.
-
-
-
-
-
-
-
-
-
-
-
-Constructor Summary
-
-
-
-
-
-
-
-Method Summary
-
-Methods
-Modifier and Type
-Method and Description
-
-
-ReadSetStats getStatsByType Get a set of stats (for either Template, Complement or 2D reads)
-
-
-
-
-
-
-Methods inherited from class java.lang.Object
-clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
-
-
-
-
-
-
-
-
-
-
-
-
-Constructor Detail
-
-
-
-
-
-
-
-
-
-
-Method Detail
-
-
-
-
-
-getStatsByType
-public ReadSetStats getStatsByType(int t)
-Get a set of stats (for either Template, Complement or 2D reads)
-Parameters: t - integer type - see defs in NanoOKOptionsReturns: ReadSetStats object
-
-
-
-
-
-
ParserRunnable
-
-JavaScript is disabled on your browser.
-
-
-
-
-
-
-
-
-
-java.lang.Object
-
-
-
-
-
-
-
-
-
-
-
-
-
-Constructor Summary
-
-
-
-
-
-
-
-Method Summary
-
-Methods
-Modifier and Type
-Method and Description
-
-
-voidrun Entry point to thread
-
-
-
-
-
-
-Methods inherited from class java.lang.Object
-clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
-
-
-
-
-
-
-
-
-
-
-
-
-Constructor Detail
-
-
-
-
-
-
-
-
-
-
-Method Detail
-
-
-
-
-
-run
-public void run()
-Entry point to thread
-
-Specified by: run in interface java.lang.Runnable
-
-
-
-
-
-
-
ProcessLogger
-
-JavaScript is disabled on your browser.
-
-
-
-
-
-
-
-
-
-java.lang.Object
-
-
-
-
-
-
-
-
-
-
-
-
-
-Constructor Summary
-
-Constructors
-Constructor and Description
-
-
-ProcessLogger
-
-
-
-
-
-
-
-Method Summary
-
-Methods
-Modifier and Type
-Method and Description
-
-
-java.util.ArrayListcheckCommand
-
-java.util.ArrayListgetCommandOutput
-
-voidrunAndLogCommand
-
-voidrunCommand
-
-voidsetWriteFormat
-
-
-
-
-
-Methods inherited from class java.lang.Object
-clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
-
-
-
-
-
-
-
-
-
-
-
-
-Constructor Detail
-
-
-
-
-
-ProcessLogger
-public ProcessLogger()
-
-
-
-
-
-
-
-
-
RGraphPlotter
-
-JavaScript is disabled on your browser.
-
-
-
-
-
-
-
-
-
-java.lang.Object
-
-
-
-
-
-
-
-
-
-
-
-
-
-Constructor Summary
-
-
-
-
-
-
-
-Method Summary
-
-Methods
-Modifier and Type
-Method and Description
-
-
-voidplot Execute plot commands.
-
-
-voidrunScript
-
-
-
-
-
-Methods inherited from class java.lang.Object
-clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
-
-
-
-
-
-
-
-
-
-
-
-
-Constructor Detail
-
-
-
-
-
-
-
-
-
-
-
RGraphRunnable
-
-JavaScript is disabled on your browser.
-
-
-
-
-
-
-
-
-
-java.lang.Object
-
-
-
-
-
-
-
-
-
-
-
-
-
-Constructor Summary
-
-Constructors
-Constructor and Description
-
-
-RGraphRunnable
-
-
-
-
-
-
-
-Method Summary
-
-Methods
-Modifier and Type
-Method and Description
-
-
-voidrun
-
-
-
-
-
-Methods inherited from class java.lang.Object
-clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
-
-
-
-
-
-
-
-
-
-
-
-
-Constructor Detail
-
-
-
-
-
-
-
-
-
-
-Method Detail
-
-
-
-
-
-run
-public void run()
-
-Specified by: run in interface java.lang.Runnable
-
-
-
-
-
-
-
ReadAligner
-
-JavaScript is disabled on your browser.
-
-
-
-
-
-
-
-
-
-java.lang.Object
-
-
-
-
-
-
-
-
-
-
-
-
-
-Constructor Summary
-
-
-
-
-
-
-
-Method Summary
-
-Methods
-Modifier and Type
-Method and Description
-
-
-voidalign
-
-voidcreateDirectories Create directories for output
-
-
-booleanisValidReadFile
-
-
-
-
-
-Methods inherited from class java.lang.Object
-clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
-
-
-
-
-
-
-
-
-
-
-
-
-Constructor Detail
-
-
-
-
-
-
-
-
-
-
-
ReadExtractor
-
-JavaScript is disabled on your browser.
-
-
-
-
-
-
-
-
-
-java.lang.Object
-
-
-
-
-
-
-
-
-
-
-
-
-
-Constructor Summary
-
-
-
-
-
-
-
-Method Summary
-
-Methods
-Modifier and Type
-Method and Description
-
-
-voidcreateDirectories Create directories for output
-
-
-voidextract Extract reads
-
-
-
-
-
-
-Methods inherited from class java.lang.Object
-clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
-
-
-
-
-
-
-
-
-
-
-
-
-Constructor Detail
-
-
-
-
-
-
-
-
-
-
-
ReadExtractorRunnable
-
-JavaScript is disabled on your browser.
-
-
-
-
-
-
-
-
-
-java.lang.Object
-
-
-nanook.ReadExtractorRunnable
-
-
-
-
-
-
-
-
-
-
-
-
-Field Summary
-
-
-
-
-
-
-
-Constructor Summary
-
-
-
-
-
-
-
-Method Summary
-
-Methods
-Modifier and Type
-Method and Description
-
-
-voidrun Extract reads of each type from file
-
-
-
-
-
-
-Methods inherited from class java.lang.Object
-clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-Constructor Detail
-
-
-
-
-
-ReadExtractorRunnable
-public ReadExtractorRunnable(NanoOKOptions o,
- java.lang.String in,
- java.lang.String file,
- java.lang.String out)
-
-
-
-
-
-
-
-
-Method Detail
-
-
-
-
-
-
-
-
-
ReadLengthsSummaryFile
-
-JavaScript is disabled on your browser.
-
-
-
-
-
-
-
-
-
-java.lang.Object
-
-
-nanook.ReadLengthsSummaryFile
-
-
-
-
-
-
-public class ReadLengthsSummaryFile
-extends java.lang.Object
-Represents a summary file containing basic information on read lengths, N50 etc. for the three different read types.
-
-
-
-
-
-
-
-
-
-
-
-Constructor Summary
-
-Constructors
-Constructor and Description
-
-
-ReadLengthsSummaryFile Constructor.
-
-
-
-
-
-
-
-
-Method Summary
-
-Methods
-Modifier and Type
-Method and Description
-
-
-voidaddReadSetStats ReadSetStats r)Output read stats for a particular type (Template, Complement, 2D).
-
-
-voidclose Close output file.
-
-
-voidopen Open output file.
-
-
-
-
-
-
-Methods inherited from class java.lang.Object
-clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
-
-
-
-
-
-
-
-
-
-
-
-
-Constructor Detail
-
-
-
-
-
-
-
-
-
-
-Method Detail
-
-
-
-
-
-
-
-
-
-addReadSetStats
-public void addReadSetStats(ReadSetStats r)
-Output read stats for a particular type (Template, Complement, 2D).
-Parameters: r - ReadSetStats object for the type
-
-
-
-
-
-
-close
-public void close()
-Close output file.
-
-
-
-
-
-
-
ReadSet
-
-JavaScript is disabled on your browser.
-
-
-
-
-
-
-
-
-
-java.lang.Object
-
-
-
-
-
-
-
-public class ReadSet
-extends java.lang.Object
-Represents a read set (Template reads, Complement reads, or 2D reads).
-
-
-
-
-
-
-
-
-
-
-
-Constructor Summary
-
-
-
-
-
-
-
-Method Summary
-
-Methods
-Modifier and Type
-Method and Description
-
-
-ReadSetStats getStats Get stats object.
-
-
-java.lang.StringgetTypeString Get type of this read set.
-
-
-intprocessReads Gather length statistics on reads and parse alignments
-
-
-
-
-
-
-Methods inherited from class java.lang.Object
-clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
-
-
-
-
-
-
-
-
-
-
-
-
-Constructor Detail
-
-
-
-
-
-
-
-
-
-
-
ReadSetStats
-
-JavaScript is disabled on your browser.
-
-
-
-
-
-
-
-
-
-java.lang.Object
-
-
-
-
-
-
-
-
-
-
-
-
-
-Constructor Summary
-
-
-
-
-
-
-
-Method Summary
-
-Methods
-Modifier and Type
-Method and Description
-
-
-voidaddDeletionError Store a deletion error.
-
-
-voidaddInsertionError Store an insertion error.
-
-
-voidaddLength Store a read length in the array of read lengths.
-
-
-voidaddReadBestKmer Store best perfect kmers for each read.
-
-
-voidaddReadFile Update count of read files.
-
-
-voidaddReadWithAlignment Store a read with an alignment.
-
-
-voidaddReadWithoutAlignment Store a read without an alignment.
-
-
-voidaddSubstitutionError Store a substitution error.
-
-
-voidcalculateStats Calculate various statistics, e.g.
-
-
-voidcloseKmersFile
-
-voidcloseLengthsFile Close the read lengths file.
-
-
-intgetLongest Get longest read in this read set.
-
-
-doublegetMeanLength Get mean length of reads in this read set.
-
-
-MotifStatistics getMotifStatistics Get motif statistics.
-
-
-intgetN50 Get N50 for this read set.
-
-
-intgetN50Count Get N50 count - number of reads of length N50 or greater.
-
-
-intgetN90 Get N90 for this read set.
-
-
-intgetN90Count Get N90 count - number of reads of length N90 or greater.
-
-
-intgetNumberOfFailFiles Get number of read files in fail directory
-
-
-intgetNumberOfPassFiles Get number of read files in pass directory
-
-
-intgetNumberOfReads Get number of reads in this read set.
-
-
-intgetNumberOfReadsWithAlignments Get number of reads with alignments in this read set.
-
-
-intgetNumberOfReadsWithoutAlignments Get number of reads without alignments in this read set.
-
-
-intgetNumberOfSubstitutions Get number of substitutions.
-
-
-intgetNumReadFiles Get number of read files.
-
-
-intgetNumReads Get number of reads.
-
-
-doublegetPercentOfReadsWithAlignments Get percentage of reads with alignments
-
-
-doublegetPercentOfReadsWithoutAlignments Get percentage of reads without alignments
-
-
-intgetReadLength Get length of read
-
-
-intgetShortest Get shortest read in this read set.
-
-
-int[][]getSubstitutionErrors Get substitution error matrix (A, C, G, T vs A, C, G, T).
-
-
-intgetTotalBases Get total bases represented by read set.
-
-
-intgetType Get type
-
-
-java.lang.StringgetTypeString Get type as a string.
-
-
-voidopenLengthsFile Open a text file to store read lengths.
-
-
-voidoutputMotifStats Write motif stats to screen.
-
-
-voidprintStats Print statistics to screen.
-
-
-voidwritekCounts
-
-voidwriteSummaryFile Write a short summary file for this read set.
-
-
-
-
-
-
-Methods inherited from class java.lang.Object
-clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
-
-
-
-
-
-
-
-
-
-
-
-
-Constructor Detail
-
-
-
-
-
-
-
-
-
-
-Method Detail
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-getType
-public int getType()
-Get type
-Returns: type
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-getNumReads
-public int getNumReads()
-Get number of reads.
-Returns: number of reads
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-addLength
-public void addLength(java.lang.String id,
- int l)
-Store a read length in the array of read lengths.
-Parameters: id - ID of readl - length
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-addSubstitutionError
-public void addSubstitutionError(java.lang.String kmer,
- char refChar,
- char subChar)
-Store a substitution error.
-Parameters: kmer - kmer prior to errorrefChar - reference basesubChar - substituted base
-
-
-
-
-
-
-getSubstitutionErrors
-public int[][] getSubstitutionErrors()
-Get substitution error matrix (A, C, G, T vs A, C, G, T).
-Returns: Substitution error matrix
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-writekCounts
-public void writekCounts(java.lang.String id,
- int length,
- int nk,
- int[] s,
- int[] kCounts)
-
-
-
-
-
-
-
ReferenceSequence
-
-JavaScript is disabled on your browser.
-
-
-
-
-
-
-
-
-
-java.lang.Object
-
-
-nanook.ReferenceSequence
-
-
-
-
-
-
-
-
-
-
-
-
-Constructor Summary
-
-Constructors
-Constructor and Description
-
-
-ReferenceSequence Constructor
-
-
-
-
-
-
-
-
-Method Summary
-
-Methods
-Modifier and Type
-Method and Description
-
-
-intcompareTo
-
-intgetBinSize Get bin size for graph plotting
-
-
-java.lang.StringgetId Get ID for this sequence.
-
-
-KmerTable getKmerTable Get kmer table
-
-
-java.lang.StringgetName Get display name for this sequence.
-
-
-intgetSize Get size (length) of this sequence.
-
-
-ReferenceSequenceStats getStatsByType Get stats for a particular type (Template, Complement, 2D).
-
-
-voidopenAlignmentSummaryFiles Open alignment summary files for each reference for each type (Template, Complement, 2D).
-
-
-voidwriteKmerFile
-
-
-
-
-
-Methods inherited from class java.lang.Object
-clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
-
-
-
-
-
-
-
-
-
-
-
-
-Constructor Detail
-
-
-
-
-
-
-
-
-
-
-Method Detail
-
-
-
-
-
-openAlignmentSummaryFiles
-public void openAlignmentSummaryFiles(java.lang.String analysisDir)
-Open alignment summary files for each reference for each type (Template, Complement, 2D).
-Parameters: analysisDir - directory to write files to
-
-
-
-
-
-
-getStatsByType
-public ReferenceSequenceStats getStatsByType(int t)
-Get stats for a particular type (Template, Complement, 2D).
-Parameters: t - integer typeReturns: ReferenceSequenceStats object
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
ReferenceSequenceStats
-
-JavaScript is disabled on your browser.
-
-
-
-
-
-
-
-
-
-java.lang.Object
-
-
-nanook.ReferenceSequenceStats
-
-
-
-
-
-
-public class ReferenceSequenceStats
-extends java.lang.Object
-Stores stats for each reference sequence, one object per read type (Template, Complement, 2D).
-
-
-
-
-
-
-
-
-
-
-
-Constructor Summary
-
-Constructors
-Constructor and Description
-
-
-ReferenceSequenceStats Constructor.
-
-
-
-
-
-
-
-
-Method Summary
-
-Methods
-Modifier and Type
-Method and Description
-
-
-voidaddAlignmentStats Store alignment stats.
-
-
-voidaddCoverage Increment coverage between two points.
-
-
-voidaddDeletionError ReadSetStats stats)Store a deletion error.
-
-
-voidaddInsertionError ReadSetStats stats)Store an insertion error.
-
-
-voidaddKmerAbundance
-
-voidaddPerfectKmer Store all perfect kmer sizes for later analysis.
-
-
-voidaddReadBestKmer Store best perfect kmer length for each read.
-
-
-voidaddSubstitutionError ReadSetStats stats)Store a substitution error.
-
-
-voidclearStats Clear all stats.
-
-
-doublegetAlignedNegativeStrandPercent Get percent of reads aligned on -ve strand
-
-
-doublegetAlignedPercentIdentical Get percent identity of aligned bases.
-
-
-doublegetAlignedPercentIdenticalWithoutIndels Get percent identity of aligned bases.
-
-
-doublegetAlignedPositiveStrandPercent Get percent of reads aligned on +ve strand
-
-
-AlignmentsTableFile getAlignmentsTableFile Get the associated AlignmentsTableFile object
-
-
-java.util.ArrayListgetKmerAbundance
-
-intgetLongestPerfectKmer Get longest perfect kmer length.
-
-
-doublegetMeanDeletionSize Get the mean deletion size
-
-
-doublegetMeanInsertionSize Get the mean insertion size
-
-
-doublegetMeanReadLength Get mean read length
-
-
-intgetNumberOfDeletionErrors Get number of deletion errors.
-
-
-intgetNumberOfInsertionErrors Getnumber of insertion errors.
-
-
-intgetNumberOfReadsWithAlignments Get number of reads with alignments.
-
-
-intgetNumberOfSubstitutionErrors Get number of substitution errors.
-
-
-doublegetPercentDeletionErrors Get percentage of deletion errors
-
-
-doublegetPercentInsertionErrors Get percentage of insertion errors
-
-
-doublegetPercentSubstitutionErrors Get percentage of substitution errors
-
-
-KmerTable getReadKmerTable
-
-doublegetReadPercentIdentical Get percent identity of read.
-
-
-intgetTotalAlignedBases Get the number of aligned bases
-
-
-voidopenAlignmentsTableFile Create an alignments table file.
-
-
-voidsortKmerAbundance
-
-voidwriteBestPerfectKmerHist Write data for best perfect kmer histogram.
-
-
-voidwriteBestPerfectKmerHistCumulative Write data for best perfect kmer cumulative histogram.
-
-
-voidwriteCoverageData Write coverage file for later graph plotting.
-
-
-voidwriteDeletionStats Write a file of deletion stats for plotting.
-
-
-voidwriteInsertionStats Write a file of insertion stats for plotting.
-
-
-voidwritePerfectKmerHist Write data for perfect kmer histogram.
-
-
-voidwriteSummary Write a line to the reference sequence summary file.
-
-
-
-
-
-
-Methods inherited from class java.lang.Object
-clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
-
-
-
-
-
-
-
-
-
-
-
-
-Constructor Detail
-
-
-
-
-
-
-
-
-
-
-Method Detail
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-clearStats
-public void clearStats()
-Clear all stats.
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-writeCoverageData
-public void writeCoverageData(java.lang.String filename,
- int binSize)
-Write coverage file for later graph plotting.
-Parameters: filename - output filenamebinSize - bin size
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-writeSummary
-public void writeSummary(java.io.PrintWriter pw,
- java.lang.String format)
-Write a line to the reference sequence summary file.
-Parameters: pw - PrintWriter object to write withformat - format string for output
-
-
-
-
-
-
-
-
-
-
-addAlignmentStats
-public void addAlignmentStats(int querySize,
- int alignedSize,
- int alignedSizeMinusIndels,
- int identicalBases,
- java.lang.String hitStrand,
- java.lang.String queryStrand)
-Store alignment stats.
-Parameters: querySize - query sizealignedSize - number of aligned basesidenticalBases - number of identical bases
-
-
-
-
-
-
-
-
-
-
-addInsertionError
-public void addInsertionError(int size,
- java.lang.String kmer,
- ReadSetStats stats)
-Store an insertion error.
-Parameters: size - - size of insertionkmer - - kmer before errorstats - - ReadSetStats associated with the error
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-addSubstitutionError
-public void addSubstitutionError(java.lang.String kmer,
- char refChar,
- char subChar,
- ReadSetStats stats)
-Store a substitution error.
-Parameters: kmer - - kmer before errorrefChar - - reference basesubChar - - substituted basestats - - ReadSetStats associated with the error
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
References
-
-JavaScript is disabled on your browser.
-
-
-
-
-
-
-
-
-
-java.lang.Object
-
-
-
-
-
-
-
-
-
-
-
-
-
-Constructor Summary
-
-
-
-
-
-
-
-Method Summary
-
-
-
-
-
-Methods inherited from class java.lang.Object
-clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
-
-
-
-
-
-
-
-
-
-
-
-
-Constructor Detail
-
-
-
-
-
-
-
-
-
-
-Method Detail
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-writeTexSummary
-public void writeTexSummary(int type,
- java.io.PrintWriter pw)
-Write reference summary to LaTeX report.
-Parameters: type - type from NanoOKOptionspw - handle to LaTeX file
-
-
-
-
-
-
ReportWriter
-
-JavaScript is disabled on your browser.
-
-
-
-
-
-
-
-
-
-java.lang.Object
-
-
-
-
-
-
-
-
-
-
-
-
-
-Constructor Summary
-
-
-
-
-
-
-
-Method Summary
-
-
-
-
-
-Methods inherited from class java.lang.Object
-clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
-
-
-
-
-
-
-
-
-
-
-
-
-Constructor Detail
-
-
-
-
-
-
-
-
-
-
-Method Detail
-
-
-
-
-
-open
-public void open()
-Open the .tex file.
-
-
-
-
-
-
-
-close
-public void close()
-Close the .tex file.
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-writeMotifRange
-public void writeMotifRange(int listType,
- int k,
- int colCount)
-Write Top 10 or Bottom 10 moitf section.
-Parameters: listType - either TYPE_TOP or TYPE_BOTTOMk - kmer size
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-makePDF
-public void makePDF()
-
-
-
-
-
-
-
SAMParser
-
-JavaScript is disabled on your browser.
-
-
-
-
-
-
-
-
-
-java.lang.Object
-
-
-
-
-
-
-
-
-
-
-
-
-
-Constructor Summary
-
-
-
-
-
-
-
-Method Summary
-
-
-
-
-
-Methods inherited from class java.lang.Object
-clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
-
-
-
-
-
-
-
-
-
-
-
-
-Constructor Detail
-
-
-
-
-
-
-
-
-
-
-
SequenceLogo
-
-JavaScript is disabled on your browser.
-
-
-
-
-
-
-
-
-
-java.lang.Object
-
-
-
-
-
-
-
-
-
-
-
-
-
-Constructor Summary
-
-Constructors
-Constructor and Description
-
-
-SequenceLogo Debugging constructor
-
-
-SequenceLogo Constructor
-
-
-
-
-
-
-
-
-Method Summary
-
-Methods
-Modifier and Type
-Method and Description
-
-
-voidaddBase Set relative counts at a given position in the logo.
-
-
-voiddrawImage Draw the logo image.
-
-
-voidsaveImage Save the logo as an image.
-
-
-
-
-
-
-Methods inherited from class java.lang.Object
-clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
-
-
-
-
-
-
-
-
-
-
-
-
-Constructor Detail
-
-
-
-
-
-
-
-
-
-SequenceLogo
-public SequenceLogo()
-Debugging constructor
-
-
-
-
-
-
-
-
-Method Detail
-
-
-
-
-
-addBase
-public void addBase(int position,
- int a,
- int c,
- int g,
- int t)
-Set relative counts at a given position in the logo.
-Parameters: position - position (0-offset)a - number of Asc - number of Csg - number of Gst - number of Ts
-
-
-
-
-
-
-drawImage
-public void drawImage()
-Draw the logo image.
-
-
-
-
-
-
-
-
-
-
-
SequenceReader
-
-JavaScript is disabled on your browser.
-
-
-
-
-
-
-
-
-
-java.lang.Object
-
-
-
-
-
-
-
-
-
-
-
-
-
-Constructor Summary
-
-Constructors
-Constructor and Description
-
-
-SequenceReader
-
-
-
-
-
-
-
-Method Summary
-
-Methods
-Modifier and Type
-Method and Description
-
-
-java.lang.StringgetID
-
-intgetLength
-
-intgetSequenceCount
-
-java.lang.StringgetSubSequence
-
-intindexFASTAFile Parse a FASTA file
-
-
-intindexFASTQFile
-
-voidstoreKmers KmerTable t)
-
-
-
-
-
-Methods inherited from class java.lang.Object
-clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
-
-
-
-
-
-
-
-
-
-
-
-
-Constructor Detail
-
-
-
-
-
-
-
-
-
-
-
SystemCommandRunnable
-
-JavaScript is disabled on your browser.
-
-
-
-
-
-
-
-
-
-java.lang.Object
-
-
-nanook.SystemCommandRunnable
-
-
-
-
-
-
-
-
-
-
-
-
-Constructor Summary
-
-Constructors
-Constructor and Description
-
-
-SystemCommandRunnable NanoOKOptions ops,
- java.lang.String msg,
- java.lang.String com,
- java.lang.String out,
- java.lang.String log)Constructor
-
-
-
-
-
-
-
-
-Method Summary
-
-Methods
-Modifier and Type
-Method and Description
-
-
-voidrun
-
-
-
-
-
-Methods inherited from class java.lang.Object
-clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
-
-
-
-
-
-
-
-
-
-
-
-
-Constructor Detail
-
-
-
-
-
-SystemCommandRunnable
-public SystemCommandRunnable(NanoOKOptions ops,
- java.lang.String msg,
- java.lang.String com,
- java.lang.String out,
- java.lang.String log)
-Constructor
-Parameters: o - program options
-
-
-
-
-
-
-
-Method Detail
-
-
-
-
-
-run
-public void run()
-
-Specified by: run in interface java.lang.Runnable
-
-
-
-
-
-
-
Uses of Class nanook.Alignment
-
-JavaScript is disabled on your browser.
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-Methods in nanook that return types with arguments of type Alignment
-Modifier and Type
-Method and Description
-
-
-
-java.util.List<Alignment >AlignmentFileParser. getHighestScoringSet Get highest scoring set of alignments (ie.
-
-
-
-
-Methods in nanook with parameters of type Alignment
-Modifier and Type
-Method and Description
-
-
-
-voidAlignmentMerger. addAlignment Alignment a)Merge in a new alignment
-
-
-
-
-
-
-
Uses of Interface nanook.AlignmentFileParser
-
-JavaScript is disabled on your browser.
-
-
-
-
-
-
-
-
-
-
-
-
-
diff --git a/dist/javadoc/nanook/class-use/AlignmentInfo.html b/dist/javadoc/nanook/class-use/AlignmentInfo.html
deleted file mode 100644
index e916241..0000000
--- a/dist/javadoc/nanook/class-use/AlignmentInfo.html
+++ /dev/null
@@ -1,165 +0,0 @@
-
-
-
-
-
-Uses of Class nanook.AlignmentInfo
-
-JavaScript is disabled on your browser.
-
-
-
-
-
-
-
-
-
-
-
-
-
diff --git a/dist/javadoc/nanook/class-use/AlignmentMerger.html b/dist/javadoc/nanook/class-use/AlignmentMerger.html
deleted file mode 100644
index 10a5ba4..0000000
--- a/dist/javadoc/nanook/class-use/AlignmentMerger.html
+++ /dev/null
@@ -1,141 +0,0 @@
-
-
-
-
-
-Uses of Class nanook.AlignmentMerger
-
-JavaScript is disabled on your browser.
-
-
-
-
-
-
-
-
-
-
-
-
-
diff --git a/dist/javadoc/nanook/class-use/AlignmentsTableFile.html b/dist/javadoc/nanook/class-use/AlignmentsTableFile.html
deleted file mode 100644
index cdc9b5f..0000000
--- a/dist/javadoc/nanook/class-use/AlignmentsTableFile.html
+++ /dev/null
@@ -1,189 +0,0 @@
-
-
-
-
-
-Uses of Class nanook.AlignmentsTableFile
-
-JavaScript is disabled on your browser.
-
-
-
-
-
-
-
-
-
-
-
-
-
diff --git a/dist/javadoc/nanook/class-use/BLASRParser.html b/dist/javadoc/nanook/class-use/BLASRParser.html
deleted file mode 100644
index bae824e..0000000
--- a/dist/javadoc/nanook/class-use/BLASRParser.html
+++ /dev/null
@@ -1,114 +0,0 @@
-
-
-
-
-
-Uses of Class nanook.BLASRParser
-
-JavaScript is disabled on your browser.
-
-
-
-
-
-
-No usage of nanook.BLASRParser
-
-
-
-
-
-
diff --git a/dist/javadoc/nanook/class-use/BWAParser.html b/dist/javadoc/nanook/class-use/BWAParser.html
deleted file mode 100644
index 4983b1f..0000000
--- a/dist/javadoc/nanook/class-use/BWAParser.html
+++ /dev/null
@@ -1,114 +0,0 @@
-
-
-
-
-
-Uses of Class nanook.BWAParser
-
-JavaScript is disabled on your browser.
-
-
-
-
-
-
-No usage of nanook.BWAParser
-
-
-
-
-
-
diff --git a/dist/javadoc/nanook/class-use/CIGARString.html b/dist/javadoc/nanook/class-use/CIGARString.html
deleted file mode 100644
index e758bc5..0000000
--- a/dist/javadoc/nanook/class-use/CIGARString.html
+++ /dev/null
@@ -1,114 +0,0 @@
-
-
-
-
-
-Uses of Class nanook.CIGARString
-
-JavaScript is disabled on your browser.
-
-
-
-
-
-
-No usage of nanook.CIGARString
-
-
-
-
-
-
diff --git a/dist/javadoc/nanook/class-use/GCCounter.html b/dist/javadoc/nanook/class-use/GCCounter.html
deleted file mode 100644
index c136aad..0000000
--- a/dist/javadoc/nanook/class-use/GCCounter.html
+++ /dev/null
@@ -1,114 +0,0 @@
-
-
-
-
-
-Uses of Class nanook.GCCounter
-
-JavaScript is disabled on your browser.
-
-
-
-
-
-
-No usage of nanook.GCCounter
-
-
-
-
-
-
diff --git a/dist/javadoc/nanook/class-use/KmerAbundance.html b/dist/javadoc/nanook/class-use/KmerAbundance.html
deleted file mode 100644
index 761dc4e..0000000
--- a/dist/javadoc/nanook/class-use/KmerAbundance.html
+++ /dev/null
@@ -1,114 +0,0 @@
-
-
-
-
-
-Uses of Class nanook.KmerAbundance
-
-JavaScript is disabled on your browser.
-
-
-
-
-
-
-No usage of nanook.KmerAbundance
-
-
-
-
-
-
diff --git a/dist/javadoc/nanook/class-use/KmerMotifStatistic.html b/dist/javadoc/nanook/class-use/KmerMotifStatistic.html
deleted file mode 100644
index 87b54ba..0000000
--- a/dist/javadoc/nanook/class-use/KmerMotifStatistic.html
+++ /dev/null
@@ -1,142 +0,0 @@
-
-
-
-
-
-Uses of Class nanook.KmerMotifStatistic
-
-JavaScript is disabled on your browser.
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-Methods in nanook with parameters of type KmerMotifStatistic
-Modifier and Type
-Method and Description
-
-
-
-voidMotifStatistics. addMotifs KmerMotifStatistic [] motif,
- java.lang.String kmer)Given a stretch of perfect sequence, store motifs at all k size.
-
-
-
-
-
-
-
Uses of Class nanook.KmerTable
-
-JavaScript is disabled on your browser.
-
-
-
-
-
-
-
-
-
-
-
-
-
diff --git a/dist/javadoc/nanook/class-use/LastParser.html b/dist/javadoc/nanook/class-use/LastParser.html
deleted file mode 100644
index d455eca..0000000
--- a/dist/javadoc/nanook/class-use/LastParser.html
+++ /dev/null
@@ -1,114 +0,0 @@
-
-
-
-
-
-Uses of Class nanook.LastParser
-
-JavaScript is disabled on your browser.
-
-
-
-
-
-
-No usage of nanook.LastParser
-
-
-
-
-
-
diff --git a/dist/javadoc/nanook/class-use/MAFAlignmentLine.html b/dist/javadoc/nanook/class-use/MAFAlignmentLine.html
deleted file mode 100644
index ce36b63..0000000
--- a/dist/javadoc/nanook/class-use/MAFAlignmentLine.html
+++ /dev/null
@@ -1,144 +0,0 @@
-
-
-
-
-
-Uses of Class nanook.MAFAlignmentLine
-
-JavaScript is disabled on your browser.
-
-
-
-
-
-
-
-
-
-
-
-
-
diff --git a/dist/javadoc/nanook/class-use/MAFParser.html b/dist/javadoc/nanook/class-use/MAFParser.html
deleted file mode 100644
index f97a2e0..0000000
--- a/dist/javadoc/nanook/class-use/MAFParser.html
+++ /dev/null
@@ -1,141 +0,0 @@
-
-
-
-
-
-Uses of Class nanook.MAFParser
-
-JavaScript is disabled on your browser.
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-Subclasses of MAFParser in nanook
-Modifier and Type
-Class and Description
-
-
-
-class LastParser Parser for LAST alignments
-
-
-
-
-
-
-
Uses of Class nanook.MarginAlignParser
-
-JavaScript is disabled on your browser.
-
-
-
-
-
-
-No usage of nanook.MarginAlignParser
-
-
-
-
-
-
diff --git a/dist/javadoc/nanook/class-use/MotifStatistics.html b/dist/javadoc/nanook/class-use/MotifStatistics.html
deleted file mode 100644
index f1128ba..0000000
--- a/dist/javadoc/nanook/class-use/MotifStatistics.html
+++ /dev/null
@@ -1,141 +0,0 @@
-
-
-
-
-
-Uses of Class nanook.MotifStatistics
-
-JavaScript is disabled on your browser.
-
-
-
-
-
-
-
-
-
-
-
-
-
diff --git a/dist/javadoc/nanook/class-use/NanoOK.html b/dist/javadoc/nanook/class-use/NanoOK.html
deleted file mode 100644
index 5174622..0000000
--- a/dist/javadoc/nanook/class-use/NanoOK.html
+++ /dev/null
@@ -1,114 +0,0 @@
-
-
-
-
-
-Uses of Class nanook.NanoOK
-
-JavaScript is disabled on your browser.
-
-
-
-
-
-
-No usage of nanook.NanoOK
-
-
-
-
-
-
diff --git a/dist/javadoc/nanook/class-use/NanoOKLog.html b/dist/javadoc/nanook/class-use/NanoOKLog.html
deleted file mode 100644
index 2440b25..0000000
--- a/dist/javadoc/nanook/class-use/NanoOKLog.html
+++ /dev/null
@@ -1,139 +0,0 @@
-
-
-
-
-
-Uses of Class nanook.NanoOKLog
-
-JavaScript is disabled on your browser.
-
-
-
-
-
-
-
-
-
-
-
-
-
diff --git a/dist/javadoc/nanook/class-use/NanoOKOptions.html b/dist/javadoc/nanook/class-use/NanoOKOptions.html
deleted file mode 100644
index b8d09a0..0000000
--- a/dist/javadoc/nanook/class-use/NanoOKOptions.html
+++ /dev/null
@@ -1,270 +0,0 @@
-
-
-
-
-
-Uses of Class nanook.NanoOKOptions
-
-JavaScript is disabled on your browser.
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-Constructors in nanook with parameters of type NanoOKOptions
-Constructor and Description
-
-
-
-AlignmentMerger NanoOKOptions o,
- ReferenceSequence r,
- int l,
- ReadSetStats s,
- int t)Constructor
-
-
-BLASRParser NanoOKOptions o,
- References r)
-
-BWAParser NanoOKOptions o,
- References r)
-
-LastParser NanoOKOptions o,
- References r)
-
-MAFParser NanoOKOptions o,
- References r)Constructor.
-
-
-MarginAlignParser NanoOKOptions o,
- References r)
-
-OverallStats NanoOKOptions o)Constructor.
-
-
-ParserRunnable NanoOKOptions o,
- ReadSetStats s,
- java.lang.String rp,
- java.lang.String ap,
- int t,
- int pf,
- AlignmentsTableFile nas)
-
-ReadAligner NanoOKOptions o,
- AlignmentFileParser afp)Constructor
-
-
-ReadExtractor NanoOKOptions o)Constructor
-
-
-ReadExtractorRunnable NanoOKOptions o,
- java.lang.String in,
- java.lang.String file,
- java.lang.String out)
-
-ReadSet NanoOKOptions o,
- ReadSetStats s)Constructor
-
-
-ReadSetStats NanoOKOptions o,
- int t)Constructor
-
-
-References NanoOKOptions o)Constructor
-
-
-ReportWriter NanoOKOptions o,
- OverallStats s)Constructor.
-
-
-RGraphPlotter NanoOKOptions o)Constructor.
-
-
-SAMParser NanoOKOptions o,
- References r)Parse a SAM file.
-
-
-SystemCommandRunnable NanoOKOptions ops,
- java.lang.String msg,
- java.lang.String com,
- java.lang.String out,
- java.lang.String log)Constructor
-
-
-
-
-
-
-
Uses of Class nanook.OverallStats
-
-JavaScript is disabled on your browser.
-
-
-
-
-
-
-
-
-
-
-
-
-
diff --git a/dist/javadoc/nanook/class-use/ParserRunnable.html b/dist/javadoc/nanook/class-use/ParserRunnable.html
deleted file mode 100644
index 8d4b1a9..0000000
--- a/dist/javadoc/nanook/class-use/ParserRunnable.html
+++ /dev/null
@@ -1,114 +0,0 @@
-
-
-
-
-
-Uses of Class nanook.ParserRunnable
-
-JavaScript is disabled on your browser.
-
-
-
-
-
-
-No usage of nanook.ParserRunnable
-
-
-
-
-
-
diff --git a/dist/javadoc/nanook/class-use/ProcessLogger.html b/dist/javadoc/nanook/class-use/ProcessLogger.html
deleted file mode 100644
index 076c6c1..0000000
--- a/dist/javadoc/nanook/class-use/ProcessLogger.html
+++ /dev/null
@@ -1,114 +0,0 @@
-
-
-
-
-
-Uses of Class nanook.ProcessLogger
-
-JavaScript is disabled on your browser.
-
-
-
-
-
-
-No usage of nanook.ProcessLogger
-
-
-
-
-
-
diff --git a/dist/javadoc/nanook/class-use/RGraphPlotter.html b/dist/javadoc/nanook/class-use/RGraphPlotter.html
deleted file mode 100644
index b40d494..0000000
--- a/dist/javadoc/nanook/class-use/RGraphPlotter.html
+++ /dev/null
@@ -1,114 +0,0 @@
-
-
-
-
-
-Uses of Class nanook.RGraphPlotter
-
-JavaScript is disabled on your browser.
-
-
-
-
-
-
-No usage of nanook.RGraphPlotter
-
-
-
-
-
-
diff --git a/dist/javadoc/nanook/class-use/RGraphRunnable.html b/dist/javadoc/nanook/class-use/RGraphRunnable.html
deleted file mode 100644
index 5220ff7..0000000
--- a/dist/javadoc/nanook/class-use/RGraphRunnable.html
+++ /dev/null
@@ -1,114 +0,0 @@
-
-
-
-
-
-Uses of Class nanook.RGraphRunnable
-
-JavaScript is disabled on your browser.
-
-
-
-
-
-
-No usage of nanook.RGraphRunnable
-
-
-
-
-
-
diff --git a/dist/javadoc/nanook/class-use/ReadAligner.html b/dist/javadoc/nanook/class-use/ReadAligner.html
deleted file mode 100644
index ace41de..0000000
--- a/dist/javadoc/nanook/class-use/ReadAligner.html
+++ /dev/null
@@ -1,114 +0,0 @@
-
-
-
-
-
-Uses of Class nanook.ReadAligner
-
-JavaScript is disabled on your browser.
-
-
-
-
-
-
-No usage of nanook.ReadAligner
-
-
-
-
-
-
diff --git a/dist/javadoc/nanook/class-use/ReadExtractor.html b/dist/javadoc/nanook/class-use/ReadExtractor.html
deleted file mode 100644
index 626f27b..0000000
--- a/dist/javadoc/nanook/class-use/ReadExtractor.html
+++ /dev/null
@@ -1,114 +0,0 @@
-
-
-
-
-
-Uses of Class nanook.ReadExtractor
-
-JavaScript is disabled on your browser.
-
-
-
-
-
-
-No usage of nanook.ReadExtractor
-
-
-
-
-
-
diff --git a/dist/javadoc/nanook/class-use/ReadExtractorRunnable.html b/dist/javadoc/nanook/class-use/ReadExtractorRunnable.html
deleted file mode 100644
index 6ab7d3d..0000000
--- a/dist/javadoc/nanook/class-use/ReadExtractorRunnable.html
+++ /dev/null
@@ -1,114 +0,0 @@
-
-
-
-
-
-Uses of Class nanook.ReadExtractorRunnable
-
-JavaScript is disabled on your browser.
-
-
-
-
-
-
-No usage of nanook.ReadExtractorRunnable
-
-
-
-
-
-
diff --git a/dist/javadoc/nanook/class-use/ReadLengthsSummaryFile.html b/dist/javadoc/nanook/class-use/ReadLengthsSummaryFile.html
deleted file mode 100644
index 43c9b64..0000000
--- a/dist/javadoc/nanook/class-use/ReadLengthsSummaryFile.html
+++ /dev/null
@@ -1,114 +0,0 @@
-
-
-
-
-
-Uses of Class nanook.ReadLengthsSummaryFile
-
-JavaScript is disabled on your browser.
-
-
-
-
-
-
-No usage of nanook.ReadLengthsSummaryFile
-
-
-
-
-
-
diff --git a/dist/javadoc/nanook/class-use/ReadSet.html b/dist/javadoc/nanook/class-use/ReadSet.html
deleted file mode 100644
index d5a9963..0000000
--- a/dist/javadoc/nanook/class-use/ReadSet.html
+++ /dev/null
@@ -1,114 +0,0 @@
-
-
-
-
-
-Uses of Class nanook.ReadSet
-
-JavaScript is disabled on your browser.
-
-
-
-
-
-
-No usage of nanook.ReadSet
-
-
-
-
-
-
diff --git a/dist/javadoc/nanook/class-use/ReadSetStats.html b/dist/javadoc/nanook/class-use/ReadSetStats.html
deleted file mode 100644
index 9fcbb57..0000000
--- a/dist/javadoc/nanook/class-use/ReadSetStats.html
+++ /dev/null
@@ -1,248 +0,0 @@
-
-
-
-
-
-Uses of Class nanook.ReadSetStats
-
-JavaScript is disabled on your browser.
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-Methods in nanook with parameters of type ReadSetStats
-Modifier and Type
-Method and Description
-
-
-
-voidReferenceSequenceStats. addDeletionError ReadSetStats stats)Store a deletion error.
-
-
-voidReferenceSequenceStats. addInsertionError ReadSetStats stats)Store an insertion error.
-
-
-voidReadLengthsSummaryFile. addReadSetStats ReadSetStats r)Output read stats for a particular type (Template, Complement, 2D).
-
-
-voidReferenceSequenceStats. addSubstitutionError ReadSetStats stats)Store a substitution error.
-
-
-intAlignmentFileParser. parseFile AlignmentsTableFile summaryFile,
- ReadSetStats overallStats)Parse an alignment file.
-
-
-intMAFParser. parseFile AlignmentsTableFile nonAlignedSummaryFile,
- ReadSetStats overallStats)Parse a LAST file.
-
-
-intSAMParser. parseFile AlignmentsTableFile nonAlignedSummaryFile,
- ReadSetStats overallStats)
-
-voidReportWriter. writeAlignmentsSection ReadSetStats stats)Write the alignments section to the report.
-
-
-
-
-Constructors in nanook with parameters of type ReadSetStats
-Constructor and Description
-
-
-
-AlignmentMerger NanoOKOptions o,
- ReferenceSequence r,
- int l,
- ReadSetStats s,
- int t)Constructor
-
-
-ParserRunnable NanoOKOptions o,
- ReadSetStats s,
- java.lang.String rp,
- java.lang.String ap,
- int t,
- int pf,
- AlignmentsTableFile nas)
-
-ReadSet NanoOKOptions o,
- ReadSetStats s)Constructor
-
-
-
-
-
-
-
Uses of Class nanook.ReferenceSequence
-
-JavaScript is disabled on your browser.
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-Constructors in nanook with parameters of type ReferenceSequence
-Constructor and Description
-
-
-
-AlignmentMerger NanoOKOptions o,
- ReferenceSequence r,
- int l,
- ReadSetStats s,
- int t)Constructor
-
-
-CIGARString ReferenceSequence hr)Constructor
-
-
-
-
-
-
-
Uses of Class nanook.ReferenceSequenceStats
-
-JavaScript is disabled on your browser.
-
-
-
-
-
-
-
-
-
-
-
-
-
diff --git a/dist/javadoc/nanook/class-use/References.html b/dist/javadoc/nanook/class-use/References.html
deleted file mode 100644
index 30eba68..0000000
--- a/dist/javadoc/nanook/class-use/References.html
+++ /dev/null
@@ -1,192 +0,0 @@
-
-
-
-
-
-Uses of Class nanook.References
-
-JavaScript is disabled on your browser.
-
-
-
-
-
-
-
-
-
-
-
-
-
diff --git a/dist/javadoc/nanook/class-use/ReportWriter.html b/dist/javadoc/nanook/class-use/ReportWriter.html
deleted file mode 100644
index 3ec8cd3..0000000
--- a/dist/javadoc/nanook/class-use/ReportWriter.html
+++ /dev/null
@@ -1,114 +0,0 @@
-
-
-
-
-
-Uses of Class nanook.ReportWriter
-
-JavaScript is disabled on your browser.
-
-
-
-
-
-
-No usage of nanook.ReportWriter
-
-
-
-
-
-
diff --git a/dist/javadoc/nanook/class-use/SAMParser.html b/dist/javadoc/nanook/class-use/SAMParser.html
deleted file mode 100644
index e2fcf64..0000000
--- a/dist/javadoc/nanook/class-use/SAMParser.html
+++ /dev/null
@@ -1,153 +0,0 @@
-
-
-
-
-
-Uses of Class nanook.SAMParser
-
-JavaScript is disabled on your browser.
-
-
-
-
-
-
-
-
-
-
-
-
-
diff --git a/dist/javadoc/nanook/class-use/SequenceLogo.html b/dist/javadoc/nanook/class-use/SequenceLogo.html
deleted file mode 100644
index 1fb06e7..0000000
--- a/dist/javadoc/nanook/class-use/SequenceLogo.html
+++ /dev/null
@@ -1,114 +0,0 @@
-
-
-
-
-
-Uses of Class nanook.SequenceLogo
-
-JavaScript is disabled on your browser.
-
-
-
-
-
-
-No usage of nanook.SequenceLogo
-
-
-
-
-
-
diff --git a/dist/javadoc/nanook/class-use/SequenceReader.html b/dist/javadoc/nanook/class-use/SequenceReader.html
deleted file mode 100644
index 5388798..0000000
--- a/dist/javadoc/nanook/class-use/SequenceReader.html
+++ /dev/null
@@ -1,114 +0,0 @@
-
-
-
-
-
-Uses of Class nanook.SequenceReader
-
-JavaScript is disabled on your browser.
-
-
-
-
-
-
-No usage of nanook.SequenceReader
-
-
-
-
-
-
diff --git a/dist/javadoc/nanook/class-use/SystemCommandRunnable.html b/dist/javadoc/nanook/class-use/SystemCommandRunnable.html
deleted file mode 100644
index 1ebe90e..0000000
--- a/dist/javadoc/nanook/class-use/SystemCommandRunnable.html
+++ /dev/null
@@ -1,114 +0,0 @@
-
-
-
-
-
-Uses of Class nanook.SystemCommandRunnable
-
-JavaScript is disabled on your browser.
-
-
-
-
-
-
-No usage of nanook.SystemCommandRunnable
-
-
-
-
-
-
diff --git a/dist/javadoc/nanook/package-frame.html b/dist/javadoc/nanook/package-frame.html
deleted file mode 100644
index 3057e93..0000000
--- a/dist/javadoc/nanook/package-frame.html
+++ /dev/null
@@ -1,61 +0,0 @@
-
-
-
-
-
-nanook
-
-
Interfaces
-
-
Classes
-
-
nanook
-
-JavaScript is disabled on your browser.
-
-
-
-
-
-Prev Package
-Next Package
-
-
-
-
-
-
-
-
-
-
-
-
-Interface Summary
-Interface
-Description
-
-
-
-AlignmentFileParser
-Interface for parsers of alignment files.
-
-
-
-
-
-
-
-Class Summary
-Class
-Description
-
-
-
-Alignment
-Generic class to represent alignment
-
-
-
-AlignmentInfo
-Class to hold information about an alignment.
-
-
-
-AlignmentMerger
-Class to merge alignments
-
-
-
-AlignmentsTableFile
-Represents alignment summary file written by tool and used for graph plotting.
-
-
-
-BLASRParser
-Parser for BLASR files
-
-
-
-BWAParser
-Parser for BWA files
-
-
-
-CIGARString
-Represent and parse a CIGAR string
-
-
-
-GCCounter
-Count GC content in references
-
-
-
-KmerAbundance
-Represent abundance of a kmer
-
-
-
-KmerMotifStatistic
-Class to store kmer motif statistics.
-
-
-
-KmerTable
-KmerTable used for 5-mer comparison
-
-
-
-LastParser
-Parser for LAST alignments
-
-
-
-MAFAlignmentLine
-Class representing an alignment line in a LAST file.
-
-
-
-MAFParser
-Parser for LAST aligner files.
-
-
-
-MarginAlignParser
-Parser for marginAlign files
-
-
-
-MotifStatistics
-Store all motif statistics (ie, insertion, deletion, substitution) at a range
- of sizes (3, 4, 5) for a single read type (Template, Complement or 2D).
-
-
-
-NanoOK
-Entry class for tool.
-
-
-
-NanoOKLog
-Logging
-
-
-
-NanoOKOptions
-Representation of program options and some global constants.
-
-
-
-OverallStats
-Represents overall (as opposed to per reference) stats for Template, Complement and 2D reads.
-
-
-
-ParserRunnable
-Enables multi-threading of parsing
-
-
-
-ProcessLogger
-Execute a system process and log result to a file
-
-
-
-ReadAligner
-Align reads
-
-
-
-ReadExtractor
-Read extractor
-
-
-
-ReadExtractorRunnable
-Enable multi-threading of read extraction
-
-
-
-ReadLengthsSummaryFile
-Represents a summary file containing basic information on read lengths, N50 etc.
-
-
-
-ReadSet
-Represents a read set (Template reads, Complement reads, or 2D reads).
-
-
-
-ReadSetStats
-Represent statistics about a read set (for example Template read set).
-
-
-
-References
-Represents the set of references (sequences) used for the analysis.
-
-
-
-ReferenceSequence
-Represents a sequence (contig) within a reference.
-
-
-
-ReferenceSequenceStats
-Stores stats for each reference sequence, one object per read type (Template, Complement, 2D).
-
-
-
-ReportWriter
-Writes a LaTeX report file.
-
-
-
-RGraphPlotter
-Executes command to plot graphs with R.
-
-
-
-RGraphRunnable
-Enable multi-threading of R plotting
-
-
-
-SAMParser
-Parser for SAM format files.
-
-
-
-SequenceLogo
-Create sequence logo (for error motifs etc.)
-
-
-
-SequenceReader
-Read FASTA files
-
-
-
-SystemCommandRunnable
-Enable multi-threading of system commands
-
-
-
-
-
-
-
-
-Prev Package
-Next Package
-
-
-
-
-
-
-
-
- nanook Class Hierarchy
-
-JavaScript is disabled on your browser.
-
-
-
-
-
-
-
-
Class Hierarchy
-
-
Interface Hierarchy
-
-
Uses of Package nanook
-
-JavaScript is disabled on your browser.
-
-
-
-
-
-
-
-
-
-
-
-
-Classes in nanook used by nanook
-Class and Description
-
-
-
-Alignment
-Generic class to represent alignment
-
-
-AlignmentFileParser
-Interface for parsers of alignment files.
-
-
-AlignmentInfo
-Class to hold information about an alignment.
-
-
-AlignmentMerger
-Class to merge alignments
-
-
-AlignmentsTableFile
-Represents alignment summary file written by tool and used for graph plotting.
-
-
-KmerMotifStatistic
-Class to store kmer motif statistics.
-
-
-KmerTable
-KmerTable used for 5-mer comparison
-
-
-MAFAlignmentLine
-Class representing an alignment line in a LAST file.
-
-
-MAFParser
-Parser for LAST aligner files.
-
-
-MotifStatistics
-Store all motif statistics (ie, insertion, deletion, substitution) at a range
- of sizes (3, 4, 5) for a single read type (Template, Complement or 2D).
-
-
-NanoOKLog
-Logging
-
-
-NanoOKOptions
-Representation of program options and some global constants.
-
-
-OverallStats
-Represents overall (as opposed to per reference) stats for Template, Complement and 2D reads.
-
-
-ReadSetStats
-Represent statistics about a read set (for example Template read set).
-
-
-References
-Represents the set of references (sequences) used for the analysis.
-
-
-ReferenceSequence
-Represents a sequence (contig) within a reference.
-
-
-ReferenceSequenceStats
-Stores stats for each reference sequence, one object per read type (Template, Complement, 2D).
-
-
-SAMParser
-Parser for SAM format files.
-
-
-
-
-
Class Hierarchy
-
-JavaScript is disabled on your browser.
-
-
-
-
-
-
-
-
Class Hierarchy
-
-
Interface Hierarchy
-
-
-#include
-#include
-#include
-#include
-
-#define VERSIONSTRING "kmer compare v0.1"
-
-unsigned int kmer_size = 0;
-unsigned int possible_kmers;
-unsigned int* read_counts = 0;
-unsigned int* ref_counts = 0;
-char* reference_filename = 0;
-char* read_filename = 0;
-char* reference_id = 0;
-
-void read_and_store_kmers(char* filename, unsigned int* counts)
-{
- FILE* fp = fopen(filename, "r");
- char line[1024];
- char id[1024];
- int reading = 0;
-
- if (!fp) {
- printf("Error: can't open %s\n", filename);
- exit(1);
- }
-
- while (!feof(fp)) {
- if (fgets(line, 1024, fp)) {
- if (line[0] == '>') {
- int i = 1;
- while ((i < strlen(line)) && (line[i] > ' ')) {
- id[i-1] = line[i];
- i++;
- }
- id[i-1] = 0;
- printf("Got ID %s\n", id);
- }
- }
- }
-
- fclose(fp);
-}
-
-void usage(void) {
- printf("Syntax: kmercompare <-r reference> <-a reads> <-k kmer> [-i id]\n");
-}
-
-void parse_command_line(int argc, char* argv[])
-{
- static struct option long_options[] = {
- {"reads", required_argument, NULL, 'a'},
- {"help", no_argument, NULL, 'h'},
- {"reference_id", required_argument, NULL, 'i'},
- {"kmer_size", required_argument, NULL, 'k'},
- {"reference", required_argument, NULL, 'r'},
- {0, 0, 0, 0}
- };
- int opt;
- int longopt_index;
-
- if (argc == 1) {
- usage();
- exit(0);
- }
-
- while ((opt = getopt_long(argc, argv, "a:hi:k:r:", long_options, &longopt_index)) > 0)
- {
- switch(opt) {
- case 'a':
- if (optarg==NULL) {
- printf("Error: [-a | --reads] option requires an argument.\n");
- exit(1);
- }
- read_filename = malloc(strlen(optarg) + 1);
- if (read_filename) {
- strcpy(read_filename, optarg);
- } else {
- printf("Error: can't allocate memory for string.\n");
- exit(1);
- }
- break;
- case 'h':
- usage();
- exit(0);
- break;
- case 'i':
- if (optarg==NULL) {
- printf("Error: [-i | --reference_id] option requires an argument.\n");
- exit(1);
- }
- reference_id = malloc(strlen(optarg) + 1);
- if (reference_id) {
- strcpy(reference_id, optarg);
- } else {
- printf("Error: can't allocate memory for string.\n");
- exit(1);
- }
- break;
- case 'k':
- if (optarg==NULL) {
- printf("Error: [-k | --kmer_size] option requires an argument.\n");
- exit(1);
- }
- kmer_size = atoi(optarg);
- break;
- case 'r':
- if (optarg==NULL) {
- printf("Error: [-r | --reference] option requires an argument.\n");
- exit(1);
- }
- reference_filename = malloc(strlen(optarg) + 1);
- if (reference_filename) {
- strcpy(reference_filename, optarg);
- } else {
- printf("Error: can't allocate memory for string.\n");
- exit(1);
- }
- break;
- default:
- printf("Error: Unknown option %c\n", opt);
- exit(1);
- break;
- }
- }
-
- if (!reference_filename) {
- printf("Error: you must specify a reference filename\n");
- exit(1);
- }
-
- if (!read_filename) {
- printf("Error: you must specify a read filename\n");
- exit(1);
- }
-
- if ((kmer_size < 3) || (kmer_size > 11)) {
- printf("Error: kmer size out of range\n");
- exit(1);
- }
-}
-
-
-int main(int argc, char* argv[])
-{
- parse_command_line(argc, argv);
-
- possible_kmers = (int)pow(4, kmer_size);
-
- printf("\n%s\n\n", VERSIONSTRING);
- printf(" kmer_size: %d\n", kmer_size);
- printf("Possible kmers: %d\n", possible_kmers);
- printf(" Reference: %s\n", reference_filename);
- printf(" Reads: %s\n", read_filename);
-
- read_counts = calloc(possible_kmers, sizeof(int));
- ref_counts = calloc(possible_kmers, sizeof(int));
- if ((!read_counts) || (!ref_counts)) {
- printf("Error: can't get memory to store counts\n");
- exit(1);
- }
-
- read_and_store_kmers(reference_filename, ref_counts);
- read_and_store_kmers(read_filename, read_counts);
-
- return 0;
-}
\ No newline at end of file
diff --git a/src/nanook/NanoOK.java b/src/nanook/NanoOK.java
index 4d29af5..5875ee8 100644
--- a/src/nanook/NanoOK.java
+++ b/src/nanook/NanoOK.java
@@ -16,6 +16,8 @@
import java.util.Locale;
import java.util.Set;
import java.util.concurrent.ThreadPoolExecutor;
+import ncsa.hdf.object.FileFormat;
+import ncsa.hdf.object.h5.H5File;
/**
* Entry class for tool.
@@ -23,7 +25,7 @@
* @author Richard Leggett
*/
public class NanoOK {
- public final static String VERSION_STRING = "v0.59";
+ public final static String VERSION_STRING = "v0.60";
public final static long SERIAL_VERSION = 3L;
/**
@@ -85,6 +87,17 @@ public static void checkDependencies() {
System.out.println(hVersion);
}
+ try {
+ H5File file = new H5File();
+ } catch (NoClassDefFoundError | UnsatisfiedLinkError e) {
+ System.out.println("");
+ System.out.println("Error: Could not initialise HDF5 classes. Check that the HDF libraries are correctly installed (and pointed to by LD_LIBRARY_PATH or DYLD_LIBRARY_PATH).");
+ System.out.println("Consult HDF documentation and/or NanoOK documentation.");
+ System.out.println("");
+ System.exit(1);
+ }
+
+
System.out.println("");
}
@@ -134,6 +147,15 @@ public static void testParser(NanoOKOptions options, OverallStats overallStats,
//System.exit(0);
}
+ /**
+ * Test HDF5 library
+ */
+ public static void testHDF(NanoOKOptions options) {
+ ReadExtractorRunnable r = new ReadExtractorRunnable(options, null, null, null);
+ String fastq = r.getFastq("/Users/leggettr/Desktop/TEST12345_ch1_file0.fast5", NanoOKOptions.TYPE_TEMPLATE);
+ System.exit(0);
+ }
+
private static void analyse(NanoOKOptions options) throws InterruptedException {
OverallStats overallStats = new OverallStats(options);
options.getReferences().setOverallStats(overallStats);
@@ -329,7 +351,7 @@ public static void main(String[] args) throws InterruptedException {
System.out.println("");
System.out.println("Checking dependencies");
checkDependencies();
-
+
if (options.getRunMode() == NanoOKOptions.MODE_EXTRACT) {
extract(options);
} else if (options.getRunMode() == NanoOKOptions.MODE_ALIGN) {
diff --git a/src/nanook/NanoOKOptions.java b/src/nanook/NanoOKOptions.java
index 4cbf428..ead91c8 100644
--- a/src/nanook/NanoOKOptions.java
+++ b/src/nanook/NanoOKOptions.java
@@ -71,12 +71,13 @@ public class NanoOKOptions implements Serializable {
private int specifiedType = TYPE_2D;
private String readsDir = "fast5";
private int returnValue = 0;
+ private int basecallIndex = -1;
public NanoOKOptions() {
- String value = System.getenv("NANOOK_SCRIPT_DIR");
+ String value = System.getenv("NANOOK_DIR");
if (value != null) {
- scriptsDir = value;
+ scriptsDir = value + File.separator + "scripts";
} else {
System.out.println("*** WARNING: You should set NANOOK_SCRIPT_DIR. Default value unlikely to work. ***");
System.out.println("");
@@ -118,6 +119,7 @@ public void parseArgs(String[] args) {
System.out.println(" e.g. -f reads/downloads if replicating Metrichor file structure");
System.out.println(" -a|-fasta specifies FASTA file extraction (default)");
System.out.println(" -q|-fastq specifies FASTQ file extraction");
+ System.out.println(" -basecallindex specifies the index of the analysis (default: latest)");
System.out.println("");
System.out.println("align options:");
System.out.println(" -s|-sample specifies sample directory");
@@ -248,6 +250,9 @@ public void parseArgs(String[] args) {
} else if (args[i].equalsIgnoreCase("-queue")) {
jobQueue = args[i+1];
i+=2;
+ } else if (args[i].equalsIgnoreCase("-basecallindex")) {
+ basecallIndex = Integer.parseInt(args[i+1]);
+ i+=2;
} else if (args[i].equalsIgnoreCase("-numthreads") || args[i].equalsIgnoreCase("-t")) {
numThreads = Integer.parseInt(args[i+1]);
i+=2;
@@ -788,4 +793,8 @@ public int getSpecifiedType() {
public boolean showAlignerCommand() {
return showAlignerCommand;
}
+
+ public int getBasecallIndex() {
+ return basecallIndex;
+ }
}
diff --git a/src/nanook/ReadExtractorRunnable.java b/src/nanook/ReadExtractorRunnable.java
index 0f9e2af..b1e56fc 100644
--- a/src/nanook/ReadExtractorRunnable.java
+++ b/src/nanook/ReadExtractorRunnable.java
@@ -15,6 +15,16 @@
import java.util.regex.Matcher;
import java.util.regex.Pattern;
+import java.util.EnumSet;
+import java.util.HashMap;
+import java.util.Iterator;
+import java.util.List;
+import java.util.Map;
+import ncsa.hdf.hdf5lib.H5;
+import ncsa.hdf.hdf5lib.structs.H5O_info_t;
+import ncsa.hdf.object.*;
+import ncsa.hdf.object.h5.*;
+
/**
* Enable multi-threading of read extraction
*
@@ -104,12 +114,108 @@ private void writeFastqFile(String id, String seq, String qual, String filename)
}
}
+ /**
+ * Get FASTQ section out of FAST5 file
+ * @param pathname path to FAST5 file
+ * @param type type of read
+ * @return multi-line String
+ */
+ public String getFastq(String pathname, int type) {
+ H5File file = null;
+ String[] fastq = null;
+
+ // Open a file using default properties.
+ try {
+ file = new H5File(pathname, FileFormat.READ);
+
+ // Find basecall group
+ H5Group grp;
+ String groupPath = new String();
+ String datasetPath = null;
+ String indexString;
+ int index = -1;
+ int i = 0;
+
+ // Default behaviour is to find latest
+ if (options.getBasecallIndex() == -1) {
+ do {
+ indexString = String.format("%03d", i);
+ grp = (H5Group)file.get("/Analyses/Basecall_2D_" + indexString);
+ if (grp != null) {
+ index=i;
+ i++;
+ }
+ } while (grp != null);
+ } else {
+ // User has specified index - check it exists
+ indexString = String.format("%03d", options.getBasecallIndex());
+ grp = (H5Group)file.get("/Analyses/Basecall_2D_" + indexString);
+ if (grp != null) {
+ index=i;
+ }
+ }
+
+ // index will = -1 if we didn't find any group
+ if (index >=0) {
+ // Make string for group
+ indexString = String.format("%03d", index);
+
+ // Build path to dataset
+ if (type == NanoOKOptions.TYPE_2D) {
+ datasetPath = "/Analyses/Basecall_2D_"+indexString+"/BaseCalled_2D/Fastq";
+ } else {
+ // Now look if we are new format (with Basecall_1D_XXX)
+ grp = (H5Group)file.get("/Analyses/Basecall_1D_"+indexString);
+ if (grp == null) {
+ // Old format
+ if (type == NanoOKOptions.TYPE_TEMPLATE) {
+ datasetPath = "/Analyses/Basecall_2D_"+indexString+"/BaseCalled_template/Fastq";
+ } else if (type == NanoOKOptions.TYPE_COMPLEMENT) {
+ datasetPath = "/Analyses/Basecall_2D_"+indexString+"/BaseCalled_complement/Fastq";
+ } else {
+ System.out.println("Error: bad type in getFastq");
+ System.exit(1);
+ }
+ } else {
+ // New format
+ if (type == NanoOKOptions.TYPE_TEMPLATE) {
+ datasetPath = "/Analyses/Basecall_1D_"+indexString+"/BaseCalled_template/Fastq";
+ } else if (type == NanoOKOptions.TYPE_COMPLEMENT) {
+ datasetPath = "/Analyses/Basecall_1D_"+indexString+"/BaseCalled_complement/Fastq";
+ } else {
+ System.out.println("Error: bad type in getFastq");
+ System.exit(1);
+ }
+ }
+ }
+
+ //System.out.println("Path: "+datasetPath);
+ Dataset ds = (Dataset)file.get(datasetPath);
+ if (ds == null) {
+ System.out.println("No dataset at "+datasetPath);
+ } else {
+ fastq = (String[])ds.getData();
+ }
+ }
+
+ file.close();
+ } catch (Exception e) {
+ e.printStackTrace();
+ }
+
+ if (fastq == null) {
+ return null;
+ } else {
+ return fastq[0];
+ }
+ }
+
/**
* Dump an individual read
* @param inputFilename filename of FAST5 file
* @param type type of read
*/
- private void dumpRead(String inputFilename, int type, String outputDir) {
+ private void dumpReadPrevious(String inputFilename, int type, String outputDir) {
ProcessLogger pl = new ProcessLogger();
ArrayList response = pl.getCommandOutput("h5dump -d "+typeStrings[type]+" "+inputFilename, true, true);
String outName = new File(inputFilename).getName();
@@ -175,6 +281,54 @@ private void dumpRead(String inputFilename, int type, String outputDir) {
}
}
+ /**
+ * Dump an individual read
+ * @param inputFilename filename of FAST5 file
+ * @param type type of read
+ */
+ private void dumpRead(String inputFilename, int type, String outputDir) {
+ String outName = new File(inputFilename).getName();
+
+ String fastqDatafield = getFastq(inputFilename, type);
+ if (fastqDatafield != null) {
+ String [] lines = fastqDatafield.split("\n");
+
+ String id = null;
+ String seq = lines[1];
+ String qual = lines[3];
+
+ if (lines[0].startsWith("@")) {
+ id = lines[0].substring(1);
+
+ // Fix IDs
+ Pattern outPattern = Pattern.compile("00000000-0000-0000-0000-000000000000(.+)");
+ Matcher outMatcher = outPattern.matcher(id);
+ if (outMatcher.find()) {
+ if (options.fixIDs()) {
+ id = id.replaceAll("^00000000-0000-0000-0000-000000000000_", "");
+ id = id.replaceAll(" ", "");
+ } else {
+ System.out.println("Warning: " + id + " is non-unqiue. Recommend re-running with -fixids option.");
+ System.out.println("");
+ }
+ }
+ } else {
+ System.out.println("Couldn't parse "+inputFilename);
+ }
+
+ if (id != null) {
+ if (options.getReadFormat() == NanoOKOptions.FASTA) {
+ writeFastaFile(id, seq, outputDir + File.separator + NanoOKOptions.getTypeFromInt(type) + File.separator + outName + "_BaseCalled_" + NanoOKOptions.getTypeFromInt(type) + ".fasta");
+ } else if (options.getReadFormat() == NanoOKOptions.FASTQ) {
+ writeFastqFile(id, seq, qual, outputDir + File.separator + NanoOKOptions.getTypeFromInt(type) + File.separator + outName + "_BaseCalled_" + NanoOKOptions.getTypeFromInt(type) + ".fastq");
+ }
+ }
+ } else {
+ System.out.println("Error: couldn't find payload in " + inputFilename);
+ }
+ }
+
+
/**
* Extract reads of each type from file
* @param inDir input directory