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HISTORY.md

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Version 2.0.3 - Jan 25, 2023

  • added proper default in defaults.vs.cnf for REFERENCE_INDIST_PRODUCE
    • fixed blank entry in complete $OUTPUT_DIR/vntr_${RUN_NAME} config
  • fixed sqlite version printing
  • now removes incomplete encoded_reads table
  • removed ALGNURL field from vcf output
  • added stats time and date entries for step 20 CONVERSION_AND_READ_COMPRESSION
  • fixed GEN_CONFIG option
  • Fixed trf2proclu
  • Revised updaterefs.pl
    • READ_LENGTH wired in
    • print_latex, print_distr, commify, nowhitespace removed
      • latex, graph production code extracted
    • removed VNTRPIPE_ from database in vcf output
    • removed SERVER argument
  • Isolated non-pipeline data summary scripts into perl/lib/Summarize
  • Re-configured input file parsing
    • support .fa, .fq, .sam, .cram extensions
    • allow mixing .fa and .fasta, .fq and .fastq
  • Added cram handling to documentation
  • Dropped bedtools requirement, it's not used
  • Changed default OUTPUT_DIR to .
    • simplify output structure for simple use cases
  • Changed reduced_db.sql script calling to be from DBI
    • extracted ATTACH DB line to remove renaming step
      • previously created relatively (meaning in install dir, probably not writable!)
      • using final db name will be absolute (meaning in output_dir)
  • Added last last last thing to migrate date and time stamps for step 20 to reduced database
  • Merged extra_index.pl into pcr_dup.pl
    • Merged step 15 into 14 in vntrseek.pl
    • pending stats table adjustment for defunct INDEX_PCR stats
  • Removed file greps from pcr_dup.pl
  • Removed some non-capturing grouping from greps in insert_reads.pl
  • Wrote ouput structure description
  • Internalized edlib

Dec 19, 2022

  • fixed imports in compress_reads.pl

Version 2.0.2 - Nov 3, 2022

  • added CLEANUP option to remove intermediates on success
  • changed DBSUFFIX to RUN_NAME
  • changed OUTPUT_ROOT to OUTPUT_DIR
  • redirected run_edges.pl and run_flnkcomp.pl output
    • removed now unused TMPDIR option
  • removed unused CLEAN option
  • removed obselete stats.pl
  • consolidated error checks after subscript calls into subprocedure
    • replaced SetError sub with FlagError
  • removed unused tmp paramater from run_edges.pl
  • hid (commented out) map_dup.pl output file DBSUFFIX.map_dup.txt
  • stopped all.clusters duplication in insert_reads.pl
    • removed now unused rotatedfolder parameter
  • removed second run of set_db_stats.pl
  • fixed time stamps around all steps
  • raised SeqReader out of VNTRseek folder
  • revised all SQLite statements for consistency, readability, and efficiency
  • created step 20 for database reduction steps
    • combination scores table from map, rank, and rankflank
    • implemented read compression in perl, potential new compressed_reads table
    • header reduction for fasta reads matching standard Illumina format
  • added edlib to build
    • modified lots of files for this
  • changed how SeqReader.pm locates seqtk
  • created FinishStep function to reduce code repetition
  • removed statistics and blocks for empty steps (6, 7, 11, 18)

Version 2.0.1 - Jul 26, 2022

  • fixed NPROCESSES internally so config is accurate
  • made support for relative input, output, and temp paths
  • added default relative paths for output and temp paths
  • separated DBSUFFIX and config paths
  • made blank DBSUFFIX field in defaults.vs.cnf
  • added DBSUFFIX to validation
  • removed BACKEND from defaults.vs.cnf
  • removed unnecssary entries in %opts/%VSCNF_FILE
    • REFERENCE extensions
    • BACKEND
  • restructured parameter backwards compatibility
  • unified parameter default value handling
  • revised config validation messages
  • sorted parameter handling sections
  • cleaned print_config and usage
  • added GEN_CONFIG option
  • revised start and end step argument parsing
  • fixed subscript config loading and unified preambles
  • reduced stderr spam in steps 1, 4, 8, 15, 17
  • reduced stdout spam in steps 3, 5, 10, 14, 15, 16
    • and in c scripts: redund2.c, joinc.c, flankalign.c
  • rewired map_dup.pl and run_flankcomp.pl to free up STDOUT
  • restructured run_trf_ng.pl to match other subscripts
    • argument passing, output
  • changed STDERRs to STDOUT where appropriate
    • warns, timestamps
  • fixed VNTR vcf output skipping first entry
  • (Dr. Benson) fixed redund bug mishandling profiles
  • added output database minimization to cleanup
  • removed unused arguments in subscript calls
    • notably insert_reads.pl
  • added output preclearing to all steps
  • moved final output to top level
  • removed many redundant output checks after vs_db_insert calls
  • removed SERVER symlinking
  • removed obselete scripts
  • cleaned out obselescent commented code
  • updated help files

Version 2.0.0 - Jul 11, 2022

  • cleaned up of run_edges.pl to reduce file io
  • instated new redund2.c to reduce time
  • removed overwrite of config file every run
  • merged disaparte changes in stale dev branches

Version 1.10.0-rc.4 - 2019

  • See previous releases for older changes