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CHANGELOG.md

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cager-misc changelog

2024-12-31

Add scripts cigar_maplen.py v1.0.a and samtool_setop.py v1.0.a.

2024-03-27

Add verbose mode to sum-up-snv.awk

Version changes:

  • sum-up-snv.awk: 0.1.c -> 0.2.a

2023-03-01

Rewrite seqator.py compeletely to add flexibility.

Version changes:

  • seqator: 2.0.a -> 3.0.a

2021-08-10

most-freq-subseq can now count subsequences either on positive strand or on both strands of input sequences (see option --both-strands). Default behaviour is to count subsequences only on positive strand.

Version changes:

  • most-freq-subseq: 1.1.b -> 1.2.a

2021-04-16

seqator now takes input files from directory ./contigs/DNA Files if directory ./contigs contains no "SPAdes-like" .dna files.

Version changes:

  • seqator: 1.0.a -> 1.1.a

2021-03-26

Moved combinator-FQ to the separate repository: https://github.com/masikol/combinator-FQ.

2021-01-21 edition

  • fasta-GC-content: output files now contains "Coverage" column.
  • fasta-GC-content: renames column "S (G or C)" to "S (degenerate)".

Version changes:

  • fasta-GC-content: 1.1.a -> 1.1.b -> 1.1.c

2021-01-21 edition

  • combinator-FQ: bug fix (combinator used to ternimate in the end if it couldn't extract ordinal number of contig from contig's name);

Version changes:

  • combinator-FQ: 1.3.e -> 1.3.f

2021-01-06 edition

  • kromsatel: fixed bug that would cause kromsatel to prefer minor amplicons over major ones.

Version changes:

  • kromsatel: 1.2.e -> 1.3.a

2020-12-03 edition

  • combinator-FQ: -o option addded.

Version changes:

  • combinator-FQ: 1.3.d -> 1.3.e

2020-12-02 edition

  • kromsatel: output files naming changed: now "cleaned" is suffix, not prefix.

Version changes:

  • kromsatel: 1.2.d -> 1.2.e

2020-11-14 edition

  • kromsatel now works 2 times faster.

Version changes:

  • kromsatel: 1.2.c -> 1.2.d

2020-11-13 edition

  • kromsatel: performance improved.

Version changes:

  • kromsatel: 1.2.b -> 1.2.c

2020-11-12 edition

  • kromsatel version 1.2.a added, then added version 1.2.b with code commented and some optimized operations.

2020-10-23 edition

  • pub: checked algorithm of finding color ballanced set of barcodes: now pub reclusters all barcodes except of the one having minimal silhouette score.

Version changes:

  • pub: 1.0.a --> 1.1.a

2020-10-15 edition

  • sum-up-snv (version 0.1.c) added.

2020-10-08 edition

  • combinator-FQ now rounds coverage with 2 trailing digits.

Version changes:

  • combinator-FQ: 1.3.c --> 1.3.d

2020-06-29 edition

  • dedupl-fastq.py added.

2020-06-14 edition

  • pub.R added.

2020-06-15 edition.

  • combinator-FQ: errorneous handling of SPADEs's NODE_1 with zero coverage fixed;

Version changes:

  • combinator-FQ: 1.3.b --> 1.3.c

2020-04-24 edition.

  • combinator-FQ: compatibility with a5 improved;

Version changes:

  • combinator-FQ: 1.3.a --> 1.3.b

2020-04-16 edition.

  • fastq-read-count: now counts number of bases additionaly;

Version changes:

  • fastq-read-count: 1.0.a --> 1.1.a;

2020-04-15 edition.

  • combinator-FQ: calculating of expected genome length is improved;

Version changes:

  • combinator-FQ: 1.2.b --> 1.3.a;

2020-04-14 edition.

  • find-seq script added;
  • NOS added;
  • packer-dna-to-fasta added;
  • seqator added;

2020-04-13 edition.

  • fasta-GC-content: format of output file changed to tab-separated table with summary in the end;
  • mean-qual script added;
  • fastq2fasta script added;
  • fastq-read-count script added;
  • dna-summary script added;
  • most-freq-subseq script added;

2020-04-10 evening edition.

  • combinator-FQ: a5-compatibility bug fixed;

Version changes:

  1. combinator-FQ: 1.2.a --> 1.2.b

2020-04-10 edition.

  • combinator-FQ: calculating of expected genome length is embedded once again -- not considering contigs multiplicity;
  • fasta-GC-content is added;

Version changes:

  1. combinator-FQ: 1.1.c --> 1.2.a

2020-03-18 edition.

  • combinator-FQ: calculating of expected genome length is disabled because it's impossible to handle high-copy replicons properly;

Version changes:

  1. combinator-FQ: 1.1.b --> 1.1.c

2020-03-09 edition.

  • combinator-FQ: calculation of expected genome length fixed;

Version changes:

  1. combinator-FQ: 1.1.a --> 1.1.b

2020-03-07 edition.

  • combinator-FQ: output file separated into three: adjacent_contigs. full_matching_log and summary;
  • combinator-FQ: A5-coverage summary bug fixed;

Version changes:

  1. combinator-FQ: 1.0.a --> 1.1.a

2020-03-06 edition.

  • combinator-FQ version 1.0.a added;