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CHANGELOG.md

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Changelog

countTags/0.6.1 (2024-11-30) [Anthony Boureux]

New

  • Output all reads matching one or more kmer in tabular and fasq format.

Fix

  • Correct default k value to 31.

countTags/0.6.0 (2024-11-30) [Anthony Boureux]

New

  • with option -r: output all data (header, sequence and quality code) to build a true fastq file
    • for now

Changes

  • Improve help and README.
  • Improve make test output.
  • better output with color
  • correct test with diff
  • Add code to debug, commented for now.

Fix

  • Correct 20241113-01 but read smaller than k.
    • error with nline counter
    • corrected with bug 20241120-01
  • Correct bug 20241120-01 not checking truncated fastq.
  • Correct 20241113-01: forget to count the current line when read smaller than k.
  • Improve comments.
  • When output reads, output only once the read.
  • The read was output each time a kmer was found in the read
  • Minor: Update doc to install with zstr lib.

Todo

  • Count twice when paired and overlapping.

countTags/0.5.2 (2020-04-19) [Anthony Boureux]

New

  • Can use now ,; to separate tag and name.

Changes

  • Improve color the make test.
  • Use namespace to avoid all std::
  • Minor: Correct g++ warnings.
  • Improve comments.

Fix

  • 20200419-01: do not output number of read in summary.
    • closed: commit 459de402587.
  • Minor: Exit with code 10 when error reading tags or fastq.
  • Minor: Correct error with submodule.
  • Zstr: Integrated correctly the submodule.

countTags/0.5.1 (2020-03-26) [Anthony Boureux]

Changes

  • Typo correction.
  • Remove require for --merge-counts when using --merge-counts-colname.
    • setting the second, set the first

Fix

  • 20200326-01 : No normalization (closed).

countTags/0.5.0 (2020-03-10) [Anthony Boureux]

Changes

  • To get statistic, use -v or --summary, remove other output to stdin other than table count.
  • Remove dirname if present in fastq filename.

countTags/0.4.7 (2020-03-10) [Anthony Boureux]

New

  • Manage Tags in gz or not format, also from STDIN.
  • Add option to analyze all kmers in tags provided.
  • Use option -o to output merged tsv files in a file, otherwise output to stdout.
  • Add option to group summary like tsv files.
  • Shell script to merge count of countTags in one file.

Fix

  • Improve help for new gzip format for TAGS.
  • Correct g++ warnings.
  • Do not need -s option, the script take care of the filename.
  • Add option nostranded, usefull in script.
  • this option exist only to avoid an empty option when testing multiple options

Other

  • Add submodule info.
  • Minor: Improve help and verbose mode.
  • Minor: fix error in usage help.
  • Add return code for function.

countTags/0.4.5 (2020-03-08) [Anthony Boureux]

  • Add option BILLION to normalyze.
  • Remove short option '-m', keep only long format.
  • Update the documentation.
  • Add normalization by KBP.
  • Improve help messages.
  • [New] Output version number in summary.

countTags/0.4.3 (2019-11-22) [Anthony Boureux]

  • Add version number to help.

countTags/0.4.2 (2019-11-22) [Anthony Boureux]

  • New option summary
  • Improve code, help.
  • [Bug] mergeTagCounts do not manage tag name in input file.

countTags/0.4 (2019-11-12) [Anthony Boureux]

  • [New] Manage paired mode rf fr and ff.
    • work only with 2 fastq.
    • [Update] fastq files as to be name _1.fastq and _2.fastq in paired mode. only way to be sure to find _1.fastq and not ..._1...
  • Improve help message.
  • [Update] Add long tag names to check error.
  • [Change] Improve error output to stderr instead of stdout.
  • [New] Add tag with long header text.
  • [Change] Add help for us to write arguments list.
  • [Change] Output information only for debug.
  • [Change] Output total factor in stderr, not in the file.

countTags/0.3.5 (2019-08-27) [Anthony Boureux]

  • Minor correction, version 0.3.5.
  • Use more explicit name for filename to output reads.
  • Print column name when merging only if verbose.
  • Add Tags list for quality.
  • Correct date for AB copyright.
  • Add GPL copyrigth to each files.
  • New column merge format.
  • [Bug] Correction for help page.
  • [New] Add option to output a column name when merge-counts option is used.
  • [Bug] Resolved bug 20180508-02.

countTags/0.3.4 (2018-07-02) [Anthony Boureux]

  • [Bug] 20180625-01 : do not manage paired fastq file in stranded mode.
    • the first pair is usually in Reverse strand : Reverse-Forward But in this case countTags do not reverse the first pair, so it can not find a tag in this file.
  • [Bug] resolved 20180508-02: use stdin only if '-'
  • [Bug] resolved Bug 20180508-01.
  • [Bug] Do not check if no tag given.

countTags/0.3.3 (2018-05-07) [Anthony Boureux]

  • Add test with stranded option.
  • Generate temporary file in /tmp during test.
  • Do all tests in makefile.
  • Improve doc.
  • [Bug] test presence fastq file (#20180328-01)
  • [Bug] Should use pclose instead of fclose.
    • The fastq file is open via popen, should close it with pclose
    • Appenrently, do not generate an error or segfault
  • [New] Add option to store --reads matching kmer.
  • [Bug] 20180329-01, 20180326-01: Resolved, can use -h or -V without error.
  • [Bugs] conflict between -i and -h|-V.

countTags/0.3.2 (2018-03-29) [Anthony Boureux]

  • Can take from stdin
  • [Bug] Output on STDERR tag shorter than Kmer.
  • Correct the code in option::parser to make it working
  • Add a file to list Bugs.
  • Add option -i to check if a tag file is present.
  • On error, should return <> 0.
  • [Bug] We do not support kmer > 32.
  • v0.2 does not manage tag shorter than kmer
  • [Bug] Add too much sequences in fasta format.
  • First Test files to improve version checking.
  • [Bug] Miss a KMER_LENGTH in last merge.
  • Keep only tag with size > tag_length.
  • Improve help in README.
  • Sum count for all fastq files.
  • Join multiple countTags results in one file.

countTags/0.3 (2018-03-27) [Anthony Boureux]

  • Reduce if test.
  • Update optionparser.h from upstream to vers. 1.7.
  • Really improve program usage.
  • Can read tags from STDIN or a file.
  • Improve usage doc.
  • [Bug] fasta name not set properly.
  • [Bug] Correct the tag number according to the line number.
  • Add a default name for tag if require by print tag-names option.
  • Add verbose option and debug print.
  • Read fasta, raw or tsv file format for tags.
  • Stop on option error.
  • Add -v|--version option.
  • Add -h option for help.
  • Say error on bad line arguments.
  • Remove unused options and update documentation.
  • First standalone version of countTags.