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ChangeLog
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2024-11-21 Thiago L. A. Miller <tmiller@mochsl.org.br>
* Version 1.1.6
* Merge pull request #11 from fvcr/master
FIX: docs/usage.rst. Typo 'bellow'
UPDATE: docs/meson.build: Use share/man/man1
* CHANGE: docs/meson.build: Use get_option('mandir')
2024-11-18 Thiago L. A. Miller <tmiller@mochsl.org.br>
* Version 1.1.5
2024-11-17 Thiago L. A. Miller <tmiller@mochsl.org.br>
* ADD: Create SECURITY.md
2024-11-16 Thiago L. A. Miller <tmiller@mochsl.org.br>
* UPDATE: meson version to 0.58.0
* ADD: generate man page by default and set install
Generate and install the man page, using docs/usage.rst by default. In
order to generate the doc site, it is necessary to setup meson with the
options '-Dsphinx_target=html' and, in that case, the extension
sphinx_rtd_theme will be mandatory.
2024-11-13 Thiago L. A. Miller <tmiller@mochsl.org.br>
* ADD: README.md: Badge for CodeQL and tag
2024-11-12 Thiago L. A. Miller <tmiller@mochsl.org.br>
* Version 1.1.4
* FIX docker.yml: Use ubuntu 24.04
* FIX: readthedocs build
Add .readthedocs.yml and docs/requirements.txt.
2024-11-11 Thiago L. A. Miller <tmiller@mochsl.org.br>
* UPDATE: Dockerfile: Use image ubuntu:24.04
* FIX: README.md: coveralls badge
* FIX: README.md: readthedocs badge
* FIX: ci.yml: Use ubuntu 24.04
* FIX: ci.yml: Install lcov for cpp-coveralls
* FIX: cluster.c (cluster): Typo 'controling'
2023-07-01 Thiago L. A. Miller <tmiller@mochsl.org.br>
* Version 1.1.3
* ADD docker.yml: Split testing and deploying steps
* CHANGE: ci.yml: Test on push branches and tags
* CHANGE: ci.yml: Always test and deploy on BRANCHES
BRANCHES: master, dev, tags. Skip deploying to dockerhub otherwise.
2023-06-29 Thiago L. A. Miller <tmiller@mochsl.org.br>
* CHANGE: abnormal.c (parse_unsorted_sam)
Remove blacklist with low-quality read querynames, because it may cause
too much RAM memory allocation. To solve running unsorted file, read it
three times: Firstly index all abnormal reads, secondly filter
low-quality fragments and thirdly dump all indexed fragments to
database.
2023-03-09 Thiago L. A. Miller <tmiller@mochsl.org.br>
* Version 1.1.2
* CHANGE: Dockerfile: multi-stage builds
Improve docker image size by using multi-stage builds.
* ADD: str.c (string_maybe_expand): 'nearest_pow'
* FIX: utils.c (xstrdup_concat, entry_set): Truncat
Deal with possible vulnerability in 'strncat' and 'strcpy' inside loop.
Replace with 'memcpy'.
2023-01-09 Thiago L. A. Miller <tmiller@mochsl.org.br>
* Version 1.1.1
* ADD: ci.yml (paths): meson.build
Test and deploy when 'meson.build' changes.
* FIX: meson.build (check): Version '>= 0.15.0'
Point out 'check' to the right version.
2022-12-12 Thiago L. A. Miller <tmiller@mochsl.org.br>
* FIX: INSTALL: meson configure
Fix ordering in meson command: 'meson build configure' to
'meson configure build'
2022-11-25 Thiago L. A. Miller <tmiller@mochsl.org.br>
* Version 1.1.0
* FIX: ci.yml (runs-on): ubuntu-18.04 to 20.04
* CHANGE: Dockerfile (FROM): ubuntu:18.04 to 20.04
* FIX: check_sider_*.c: Handle SIGABRT and SIGSEGV
It is not reproducible to catch SIGABRT and SIGSEGV separately, so
we overload those signals and return a EXIT_FAILURE.
* FIX: tests/check_sider_*.c: libcheck version
Drop 'setup_signal' and use native 'libcheck' to handle signals and exit
codes.
2022-11-24 Thiago L. A. Miller <tmiller@mochsl.org.br>
* FIX: ci.yml: Deprecating save-state
Move from echo echo "::set-output name={name}::{value}" to
echo "{name}={value}" >> $GITHUB_OUTPUT.
* ADD: README.pm: Docker badge
* ADD: ci.yml (paths): Filter.c, .h and Dockerfile
* ADD: ci.yml (docker): Build and deploy image
* CHANGE: ci_meson.yml: ci.yml
2022-11-23 Thiago L. A. Miller <tmiller@mochsl.org.br>
* FIX: db_merge.c (db_merge): 'in-place' error
When using the option '--in-place', all the databases are merged into
the first one of the list. In order to avoid that the same exon is
stored twice, we index the values in a hash. An error arise about the
'ense id', because the values already stored in the database to merge
to are not taken into acount.
Try to fix it indexing the pre-recorded values before starting to merge
the databases.
* CHANGE: README.md: Drop travis, dockerhub badges
* REMOVE: .travis.yml: Migrate to github actions
* ADD: .github/workflows/ci_meson.yml
2022-06-17 Thiago L. A. Miller <tmiller@mochsl.org.br>
* UPDATE: CITATION.cff: Citing article
Citing article instead of software. Use the 'preferred-citation' in
order to make Github show the citation of the published paper.
2022-06-16 Author Thiago L. A. Miller <tmiller@mochsl.org.br>
* ADD: CITATION.cff: Citation File Format (CFF)
2021-08-13 bioinfomochsl <dtohara@mochsl.org.br>
* Merge pull request #2 from ceciliaromaro/patch-3
Update usage.rst
* Merge pull request #3 from ceciliaromaro/patch-2
Update install.rst
* Merge pull request #4 from ceciliaromaro/patch-1
Update README.md
2021-08-06 ceciliaromaro <31550800+ceciliaromaro@users.noreply.github.com>
* Update usage.rst
bellow -> below
Tips
Memory consumption warning.
* Update install.rst
$ sudo apt install meson
Or "$ pip3 install --user meson" But in this case, remember to set the environment
variables.
2021-08-03 ceciliaromaro <31550800+ceciliaromaro@users.noreply.github.com>
* Update README.md
The command "pip3 install --user meson" may require setting the environment variable.
This one "sudo apt install meson" doesn't require it.
2020-08-11 Thiago L. A. Miller <tmiller@mochsl.org.br>
* Version 1.0.0
* UPDATE: AUTHORS, docs/authors.rst: Author names
* ADD: README.md (Citation): Citation in BibTeX
* ADD: *.[ch]: Attach the copying notices header
* ADD: docs/intro.rst (Citation): Citation in BibTeX
* UPDATE: docs/usage.rst (General Syntax)
* UPDATE: docs/result.rst (Results)
* UPDATE: check_sider_main.c (main): Control log
Enable and disable log verbosity according to the environment variable
in the macro LOG_DEBUG_KEY
* CHANGE: merge_call.c (DEFAULT_SUPPORT): 1
Disbale reclustering (support filtering) by default
* FIX: vcf.c (genotype_likelihood): 0,0,0
Set genotype to ./. when the probabilities are 0,0,0
2020-08-05 Thiago L. A. Miller <tmiller@mochsl.org.br>
* UPDATE: fasta.c: Use 'gz' interface
* CHANGE: gz.c: Make (GzFile *) public
* UPDATE: gff.c: Use 'gz' interface
* UPDATE: bed.c: Use 'gz' interface
2020-08-03 Thiago L. A. Miller <tmiller@mochsl.org.br>
* ADD: utils.c (buf_expand, entry_set): Control buf
Remove duplicated code by adding these functions to the utils.c
2020-08-01 Thiago L. A. Miller <tmiller@mochsl.org.br>
* ADD: gz.c: Add wrapper for libz
2020-07-29 Thiago L. A. Miller <tmiller@mochsl.org.br>
* ADD: main.c (print_citation): Show citation
Add citation option. Print it in BibTeX format
* FIX: vcf.c (genotype_likelihood): Be conservative
Restructure the genotyping. Compare doubles using 'fequal' and when in
case of equality, follow the table:
HOR HET HOA GENOTYPE
2 2 2 0/1
2 2 1 0/0
2 1 2 0/0
1 2 2 0/1
* ADD: utils.c (fequal): Compare float points
* UPDATE: process_sample.c, docs/usage.rst: Help
Update the argument 'annotation-file' help. Explain about the fields
required and about the lines that are filtered
2020-07-28 Thiago L. A. Miller <tmiller@mochsl.org.br>
* FIX: gff.c (gff_read): Spaces into GTF attr
Solve bug when reading GTF, possibly GFF3 as well, and there is a space
into the attr value: gene_name "My gene name". Now, the attr value will
correctly split it as: key=gene_name and value='My gene name'
2020-07-26 Thiago L. A. Miller <tmiller@mochsl.org.br>
* UPDATE: docs/result.rst: Start of text/imgs/codes
2020-07-23 Thiago L. A. Miller <tmiller@mochsl.org.br>
* FIX: .travis.yml: meson version
meson 0.55.0 fails when the option '-Db_coverage=true' is set
* ADD: docs/intro.rst: Add CRAM
* ADD: docs/method.rst: A new paragraph at beginning
2020-07-22 Thiago L. A. Miller <tmiller@mochsl.org.br>
* FIX: docs/usage.rst (A Practical Workflow)
Now sideRETRO works with CRAM format, so fix and update this example of
usage
* ADD: docs/usage.rst (Dealing with CRAM format)
* UPDATE: *.c: Include CRAM to the input files
* FIX: main.c: Typo in the help message
* FIX: meson.build: This closes #1
* UPDATE: docs/conf.py: Update year
2020-05-24 Thiago L. A. Miller <tmiller@mochsl.org.br>
* FIX: abnormal.c (dump_alignment): (long) core.pos
core.pos, in more recent versions of htslib, is declared as long int,
and not as int. So, cast core.pos to long int, in order to avoid gcc
warnings
2020-04-02 Thiago L. A. Miller <tmiller@mochsl.org.br>
* FIX: abnormal.c (sam_rewind): Working with CRAM
2020-03-26 Thiago L. A. Miller <tmiller@mochsl.org.br>
* Version 0.14.1
* FIX: meson.build: Make config.h before compiling
'config.h' is dynamically generated from template 'config.h.in', so it
need to be made before compiling. In order to assure the required order,
declare 'config.h' as a dependency of library and executable
2020-03-24 Thiago L. A. Miller <tmiller@mochsl.org.br>
* FIX: intro.rst (Features): Typo in 'Strandness'
* FIX: merge_call.c (merge_call_init): phred_quality
Set .phred_quality attribute to the default value at macro
DEFAULT_PHRED_QUALITY. Previous it was set to 0
2020-01-31 Thiago L. A. Miller <tmiller@mochsl.org.br>
* FIX: Dockerfile: Install git
2020-01-04 Thiago L. A. Miller <tmiller@mochsl.org.br>
* ADD: docs/meson.build (doc_images): barbara.jpg
2019-12-31 Thiago L. A. Miller <tmiller@mochsl.org.br>
* Version 0.14.0
2019-12-30 Thiago L. A. Miller <tmiller@mochsl.org.br>
* FIX: make_vcf.c: Aspell fix spelling errors
* FIX: merge_call.c: Aspell fix spelling errors
* FIX: process_sample.c: Aspell fix spelling errors
* FIX: docs/*.rst: Aspell fix spelling errors
* FIX: usage.rst (A Practical Workflow): Analysis results
* ADD: analyser.pl
2019-12-30 Thiago L. A. Miller <tmiller@mochsl.org.br>
* CHANGE: intro.rst: Functionalities -> Features
* CHANGE: README.md: Getting Started
2019-12-29 Thiago L. A. Miller <tmiller@mochsl.org.br>
* FIX: intro.rst: Typo
* ADD: README.md: Documentation
* ADD: retrocopy.rst: Complete references
* ADD: usage.rst: Usage and examples
* ADD: result.rst: Finish analysis topic
* ADD: result.rst: Download simulation data
* ADD: result.rst: Analysis confusion matrix
2019-12-28 Thiago L. A. Miller <tmiller@mochsl.org.br>
* ADD: result.rst: Analysis heatmap image
* ADD: result.rst: Running sideRETRO
2019-12-27 Thiago L. A. Miller <tmiller@mochsl.org.br>
* ADD: result.rst: Dataset and simulation topics
2019-12-26 Thiago L. A. Miller <tmiller@mochsl.org.br>
* ADD: retrocopy.rst: Retrocopy in a nutshell
2019-12-25 Thiago L. A. Miller <tmiller@mochsl.org.br>
* ADD: README.md: Dockerhub badge
* ADD: Dockerfile: docker image
* FIX: method.rst: Change Wikipedia to paper links
* CHANGE: footer.html: Style of button = normal
2019-12-24 Thiago L. A. Miller <tmiller@mochsl.org.br>
* ADD: footer.html: Extend RTD footer with COPYING message
* ADD: legalcode.txt: COPYING for documentation
* CHANGE: method.rst: References + Further Reading
2019-12-23 Thiago L. A. Miller <tmiller@mochsl.org.br>
* ADD: method.rst: Orientation
2019-12-22 Thiago L. A. Miller <tmiller@mochsl.org.br>
* ADD: method.rst (Genotype): More details and image
Explain in more details the genotype likelihoods, including the formula
derivations and an illustrative image
2019-12-20 Thiago L. A. Miller <tmiller@mochsl.org.br>
* ADD: method.rst: Genotype
2019-12-11 Thiago L. A. Miller <tmiller@mochsl.org.br>
* ADD: method.rst: Clustering
2019-12-09 Thiago L. A. Miller <tmiller@mochsl.org.br>
* ADD: method.rst: Abnormal alignments
2019-12-06 Thiago L. A. Miller <tmiller@mochsl.org.br>
* ADD: intro.rst: Host gene and make-vcf subcommand
2019-11-23 Thiago L. A. Miller <tmiller@mochsl.org.br>
* FIX: install.rst: Add 'Installing Meson'
2019-11-19 Thiago L. A. Miller <tmiller@mochsl.org.br>
* CHANGE: README.md: Add sideRETRO logo
* ADD: logo_sideRETRO.png
* ADD: install.rst: Installation page
* FIX: intro.rst: How it works
* ADD: README.md: readthedocs badge
* ADD: intro.rst: Introduction page
2019-11-16 Thiago L. A. Miller <tmiller@mochsl.org.br>
* ADD: docs: Documentation using sphinx
2019-12-25 Thiago L. A. Miller <tmiller@mochsl.org.br>
* ADD: make_vcf.c: Improve help message
* ADD: merge_call.c: Improve help and defaults
* ADD: process_sample.c: Improve help and defaults
* ADD: main.c: Improve help message
2019-12-24 Thiago L. A. Miller <tmiller@mochsl.org.br>
* FIX: utils.c (path_file): Remove extension at last dot
2019-12-19 Thiago L. A. Miller <tmiller@mochsl.org.br>
* FIX: retrocopy.c: Same parental in overlapped rtc
When two overlapped clusters share the same parental gene - maybe the
edge points are reachable, not core points (DBSCAN) - it would be
annotated as overlapped parentals. Now it will be annotated as PASS and
the parental gene name wont be duplicated (e.g. PTEN/PTEN)
* FIX: genotype.c (cross_insertion_point): ref evid
Evidence for reads covering the reference allele is calculated now by
the overlapping between read range and insertion point +/- read half
decil. It is necessary in order to avoid superextimation of reads
covering the reference allele due to mapping errors
2019-12-06 Thiago L. A. Miller <tmiller@mochsl.org.br>
* REMOVE: genotype.c, merge_call.c: --crossing-reads
* ADD: process_sample.c, merge_call.c: Final messages
2019-12-05 Thiago L. A. Miller <tmiller@mochsl.org.br>
* ADD: db.c, genotype.c vcf.c: INFO DP2
Add reference and alternate depth counts to VCF's info
2019-12-03 Thiago L. A. Miller <tmiller@mochsl.org.br>
* CHANGE: db.c, genotype.c, vcf.c: Genotype likelihood
Implement the genotype estimation by using the likelihood approach as it
is defined in Heng Li paper: "A statistical framework for SNP calling,
mutation discovery, association mapping and population genetical
parameter estimation from sequencing data - 2.2 (eq2)"
2019-11-28 Thiago L. A. Miller <tmiller@mochsl.org.br>
* Version 0.13.0
2019-11-27 Thiago L. A. Miller <tmiller@mochsl.org.br>
* ADD: make_vcf.c: make-vcf command
* FIX: vcf.c: Some typos in variable names
2019-11-26 Thiago L. A. Miller <tmiller@mochsl.org.br>
* ADD: genotype.c (genotype): phred_qualit
Filter reads crossing insertion point also by phred quality score
2019-11-25 Thiago L. A. Miller <tmiller@mochsl.org.br>
* FIX: vcf.c: Change fprintf to xfprintf
* FIX: vcf.c (vcf_print_header): Add array_free()
* ADD: check_sider_vcf.c: Tests for vcf.c interface
* ADD: vcf.c (vcf_index_fasta): VCF's REF field
Index FASTA file if passed by the user and use it for annotate the REF's
field. Also include the contig metadata at the header for each
chromosome
* ADD: fasta.c interface: Read FASTA file
* ADD: str.h (string_reset): Macro for reset string
* FIX: str.c (string_concat): strncat -> memcpy
strncat is too slow, so implement concatenation with memcpy
2019-11-23 Thiago L. A. Miller <tmiller@mochsl.org.br>
* ADD: vcf.c: Print host information
Add INFO: EXONIC, INTRONIC and NEAR. EXONIC/INTRONIC annotate host gene
detail. We choose to use separated flags, because a retrocopy can be
exonic and intronic at the same time - Overlapped parental genes,
multiple isoforms. NEAR is used for intergenic retrocopy near some
gene
2019-11-21 Thiago L. A. Miller <tmiller@mochsl.org.br>
* ADD: vcf.c interface. Write VCF file as output
2019-11-19 Thiago L. A. Miller <tmiller@mochsl.org.br>
* ADD: db.c, genotype.c: (reference_depth)
Save the reference depth for the absence of a retrocopy event. It will
be useful later when making the annotated outputs
2019-11-16 Thiago L. A. Miller <tmiller@mochsl.org.br>
* ADD: merge_call.c (merge_call_print)
* ADD: process_sample.c (process_sample_print)
2019-11-15 Thiago L. A. Miller <tmiller@mochsl.org.br>
* ADD: merge_call.c (MergeCall): struct
* ADD: process_sample.c (ProcessSample): struct
Add ProcessSample struct in order to hold all option values. Create
methods to init, destroy and validate the data. This way, things get
more organized and make it easier to dump the log values of the run
* FIX: merge_call.c (merge_call): Stop if no cluster
* FIX: process_sample.c, merge_call.c: Improve usage
2019-11-14 Thiago L. A. Miller <tmiller@mochsl.org.br>
* Version 0.12.0
* REMOVE: align.c, bwa.c: BWA subproject
Remove bwa subproject, because it won't be used any longer
2019-11-13 Thiago L. A. Miller <tmiller@mochsl.org.br>
* FIX: .travis.yml: Change (-t) timeout 2 -> 3
* ADD: genotype.c (dump_genotype): Save genotype
* FIX: genotype.c (prepare_genotype_query_stmt)
Add DISTINCT clause to SQL query in order to remove duplicated entries
* ADD: merge_call.c (genotype): Genotyping step
Add genotype step and its options: --threads and --crossing-reads
* CHANGE: genotype.c: max_cross -> crossing_reads
* ADD: retrocopy.c (retrocopy): Option for near gene
Add option --near-gene-distance in order to make dynamic the MAX_DIST
value
* ADD: genotype.c (clean_genotype_table)
2019-11-12 Thiago L. A. Miller <tmiller@mochsl.org.br>
* FIX: genotype.c (zygosity): hts_idx_destroy
Clean up memmory leak in hts_idx_t
* FIX: check_sider_{genotype,gff,wrapper}.c
Memmory leaks in test
* FIX: .travis.yml: Turn off libcheck timeout
* ADD: check_sider_genotype.c test
* ADD: genotype.c (max_cross, db_insert_genotype)
Add option max_cross (override MAX_CROSS). And finally, dump genotype to
database
* ADD: db.c (db_{prepare,insert}_genotype): genotype
2019-11-11 Thiago L. A. Miller <tmiller@mochsl.org.br>
* FIX: README.md (coveralls badge): master branch
* ADD: genotype.c (zygosity_{indexed,linear}_search)
If the BAM index is found, perform a fast search for each retrocopy
region, else index all regions inside an intervalar tree and make a slow
linear search all over the file
2019-11-09 Thiago L. A. Miller <tmiller@mochsl.org.br>
* ADD: genotype.c interface
* FIX: retrocopy.h: include db.h
2019-11-07 Thiago L. A. Miller <tmiller@mochsl.org.br>
* Version 0.11.0
* ADD: process_sample.c: --deduplicate option
* ADD: merge_call.c (merge_call): Run retrocopy step
* ADD: cluster.c (prepare_query_stmt): test type
The dedup step set the alignment type to ABNORMAL_NONE flag if the read
is a duplication. So, in the clustering step, it is necessary to avoid
using those duplicated reads
* ADD: check_sider_dedup.c test
2019-11-04 Thiago L. A. Miller <tmiller@mochsl.org.br>
* ADD: dedup.c interface: Remove duplicated reads
Add deduplication capability. Remove duplicated reads but one, which is
called the primary read. Other tools, specilized in remove duplications,
use some metric to choose the primary reads. For us, it is just
interesting the coordinates, so the primary reads are choosen randomly -
mostly the first one to appear
* ADD: abnormal.c (abnormal_classifier): Dup filter
Add filter for PCR or optical duplicated reads
2019-10-31 Thiago L. A. Miller <tmiller@mochsl.org.br>
* FIX: cluster.c, retrocopy.c (qname, source_id idx)
There is the possibility that different BAM files share reads with the
same query name. In order to avoid a mess to find the right mate, use
the source_id along with qname when required to match reads from the
same fragment
2019-10-27 Thiago L. A. Miller <tmiller@mochsl.org.br>
* ADD: retrocopy.c (clean_retrocopy_tables)
* ADD: retrocopy.c (calculate_orientation)
* FIX: meson.build: sqlite3 version 3.28.0
Change sqlite3 minimum version to 3.28.0 in order to support RANK()
functions
* ADD: check_sider_retrocopy.c test
Add test for 'retrocopy.c'. Also '.travis.yml' now prints all relevant
error logs
* ADD: retrocopy.c (merge_cluster)
Add merge_cluster function in order to populate 'cluster_merging' table
and classify retrocopy level.
Begin annotate_retrocopy function. For now it is capable to calculate
the insertion point
* ADD: db.c (db_{prepare, insert}_retrocopy)
2019-10-24 Thiago L. A. Miller <tmiller@mochsl.org.br>
* Version 0.10.0
* FIX: cluster.c (cluster): Clean tables before run
Clean clustering tables if a db exists in mc step
* CHANGE: process_sample.c: --max-base-frac -> freq
* FIX: cluster.c (prepare_filter_support_stmt): sid
Fix query statement by adding cluster.sid to grouping by
* CHANGE: merge_call.c (--gff-feature): -F -> -T
* ADD: gff.h (gff_filter_[hard|soft]_attribute_size)
2019-10-23 Thiago L. A. Miller <tmiller@mochsl.org.br>
* ADD: cluster.c, merge_call.c: --blacklist-padding
Option to increase the blacklisted regions (left and right) by N bases
2019-10-22 Thiago L. A. Miller <tmiller@mochsl.org.br>
* ADD: check_sider_blacklist.c
* ADD: exon.c (exon_tree_index_dump): GffFilter
* FIX: cluster.c (prepare_query_stmt): rlen == 0
* ADD: blacklist.c, merge_call.c: GffFilter
* ADD: gff.c (gff_filter_insert_feature)
2019-10-21 Thiago L. A. Miller <tmiller@mochsl.org.br>
* FIX: abnormal.c (dump_alignment): rlen == 0
* ADD: gff.c (gff_looks_like_gff_file): GFF filename
Test if the filename seems to belong to a GFF/GFF3/GTF file
* FIX: db.c (db_create_tables): Composite PK
Add cluster_sid references cluster(sid) to foreign keys and primary keys
into the table 'cluster_merging'
2019-10-20 Thiago L. A. Miller <tmiller@mochsl.org.br>
* ADD: cluster.c, db.c, blacklist.c: Filter column
Add cluster filter: CHR, DIST, REGION, SUPPORT, NONE. The philosophy now
is to keep all clusters and subclusters and add a new column to handle
the filtering steps
2019-10-15 Thiago L. A. Miller <tmiller@mochsl.org.br>
* ADD: gff.c (gff_filter_*)
Add gff filtering capabilities. The user must initiate a type GffFilter
with the feature_type to be filtered (e.g. gene, transcript, exon) and
may add attributes aswell (e.g. gene_type=protein_coding). The
attributes are hard and soft - which mean, hard attributes must all
match the pattern (AND); soft attributes, at least, must match one
pattern (OR).
Increase the 'gff.c' testing coverage and change the function name
'gff_open' to 'gff_open_for_reading'
2019-10-14 Thiago L. A. Miller <tmiller@mochsl.org.br>
* ADD: blacklist.c
Add blacklist interface and tables blacklist, overlapping_blacklist. The
interface was inspired in 'exon.c' way. Also add more command-line
options for indexing blacklisted regions from GTF/GFF3/BED files
2019-10-12 Thiago L. A. Miller <tmiller@mochsl.org.br>
* ADD: bed.c: Handle BED file format
2019-10-10 Thiago L. A. Miller <tmiller@mochsl.org.br>
* ADD: cluster.c (reclustering): genotype support
Add reclustering step in order to filtering low number of reads comming
from a given source (BAM). When those reads are removed, may occur that
the cluster become rarefied, and therefore, invalid according to DBSCAN
constraints.
The option --genotype-support has been added to control the low number
of reads comming from a source
2019-10-07 Thiago L. A. Miller <tmiller@mochsl.org.br>
* ADD: log.h (__FILENAME__): Macro for filename
* CHANGE: db.c, cluster.c (cluster table)
Move gene_name from clustering to cluster and add the window start and
end information
2019-10-06 Thiago L. A. Miller <tmiller@mochsl.org.br>
* CHANGE: db.c (schema table)
Change DB_SCHEMA_VERSION (float) by two integer values (%d.%d)
DB_SCHEMA_MAJOR_VERSION and DB_SCHEMA_MINOR_VERSION
2019-10-05 Thiago L. A. Miller <tmiller@mochsl.org.br>
* Version 0.9.0
* FIX: cluster.c, db.c, merge_call.c, recluster.c
Remove 'recluster.c' and merge its functionality to 'cluster.c'.
Catch all alignments whose mate overlaps a given exon and filter them
by: blacklisted chromosomes (e.g. chrM); read cannot be exonic from its
own parental; distance from its own parental gene.
Reshape database schema removing reclustering table and add retrocopy
and related tables to make relation among retrocopies and clusters
2019-09-30 Thiago L. A. Miller <tmiller@mochsl.org.br>
* ADD: correlation.c interface
Add statistics pearson and spearman correlation brought from GSL
2019-09-29 Thiago L. A. Miller <tmiller@mochsl.org.br>
* FIX: db.c (db_create_tables): foreign key
2019-09-25 Thiago L. A. Miller <tmiller@mochsl.org.br>
* FIX: process_sample.c: int -> float max_base_frac
* ADD: abnormal.c, process_sample.c (max-base-frac)
Filter reads according to the base frequency fraction in order to avoid
aligments against genome repetitive motifs
2019-09-22 Thiago L. A. Miller <tmiller@mochsl.org.br>
* FIX: cluster.c (prepare_query_stmt): blacklist_chr
Avoid clusters from and to the chromosomes into blacklist_chr set
2019-09-16 Thiago L. A. Miller <tmiller@mochsl.org.br>
* FIX: dbscan.c (dbscan_cluster): Same point shared
* DBSCAN is not entirely deterministic: border points that are
reachable from more than one cluster can be part of either
cluster, depending on the order the data are processed.
(Wikipedia)
* Fix the REACHABLE points which are shared among multiple clusters
2019-09-15 Thiago L. A. Miller <tmiller@mochsl.org.br>
* FIX: db.c (clustering table)
Fix foreign key issue by adding the clustering id as part of the weak
key. Add gene_name as parental_gene_name in order to facilitate future
analysis
* FIX: recluster.c (prepare_query_stmt): cluster_id
Change cluster_id to id
* FIX: merge_call.c (merge_call): reclustering_stmt
Call db_finalise for reclustering_stmt
* ADD: recluster.c interface
Add reclustering step in order to validate the clusters found. The
clusters will be analysed according to distance from, number of, and
number of reads for reclustering each putative parental gene
2019-09-13 Thiago L. A. Miller <tmiller@mochsl.org.br>
* ADD: db.c: reclustering table
Add reclustering table to hold validated clustering entries
* CHANGE: db.c (db_insert_clustering): rm cluster_id
Remove cluster_id from clustering table schema. Now it became a weak
entity
* ADD: merge_call.c, cluster.c (blacklist_chr)
Add option to avoid clustering at certain chromosomes. By default it
avoides 'chrM'
* ADD: set.c (set_is_member)
* CHANGE: chr.c (CHR_BUFSIZ): 32
2019-09-10 Thiago L. A. Miller <tmiller@mochsl.org.br>
* Version 0.8.0
* CHANGE: INSTALL.md -> INSTALL
* ADD: meson.build (vcs_tag)
Dynamically generate the VERSION macro according to git tag and commit
SHA-1
2019-09-09 Thiago L. A. Miller <tmiller@mochsl.org.br>
* FIX: exon.c (exon_tree_lookup_dump): Thread-safe
The alignment_id was included inside ExonTree object, which in turn was
shared among all threads. With no mutex, may occur shocking among all
alignment_id values. In order to fix it, a new private struct keeps
ExonTree and alignment_id separately
* ADD: abnormal.c, exon.c, process_sample.c: loginfo
Improve log messages for debugging and change attribute name num_threads
in AbnormalArg to inc_step - this way is more descriptive about its
function
2019-09-08 Thiago L. A. Miller <tmiller@mochsl.org.br>
* FIX: db.c (db_create_tables): source foreign key
* CHANGE: Move from Autotools to Meson build system
* REMOVE: Autotools
2019-09-06 Thiago L. A. Miller <tmiller@mochsl.org.br>
* ADD: cluster.c (index_alignment_qname)
Add index for alignment qname for speed up query. Update
prepare_query_stmt() in order to avoid the abnormal reads that
fall into their on parental gene
2019-09-05 Thiago L. A. Miller <tmiller@mochsl.org.br>
* ADD: --phred-quality option
Add phred quality score filter option in order to avoid low mapped
quality reads