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con-hi changelog

2024-12-22 edition

Version 3.3.c

Improved logging messages.

2024-12-04 edition

Version 3.3.b

Improved progress reporting.

Version 3.3.a

  1. Added option -r / --target-seq-ids. One can use it to avoid wasting time annotating all sequences in a target fasta file if some of them are unwanted. Or to annotate sequences in a multi-fasta file separately (e.g. with different thresholds) without splitting the fasta file.

  2. Now, con-hi.py runs samtools depth for each target sequence separately thus avoiding creation of large TSV files of coverage values.

  3. Now, con-hi.py runs samtools depth with option -a instead of -aa. Indeed, this option means “Output absolutely all positions, including unused ref seqs”, which isn’t helpful.

2023-12-18 edition

Version 3.2.a

Rename “consensus-highlighter” to “con-hi” for the sake of simplicity.

2023-11-01 edition

Version 3.1.b

Now, when outputting sequence records, the program will just print emerging generic Biopython warning in a human-friendly way, without extra technical lines.

In other words, instead of this:

BiopythonWarning: Increasing length of locus line to allow long name. This will result in fields that are not in usual positions.
  warnings.warn(

the program will print this warning message:

! Warning: Increasing length of locus line to allow long name. This will result in fields that are not in usual positions.

What is more important, sole catching Biopython warnings will not now cause empty output files.

2023-10-29 edition

Version 3.1.a

  1. Fix a bug that would cause the program to terminate if -C threshold is enabled and a high-coverage region starts at position 0 or ends at position (LENGTH-1) of the reference sequence.

  2. Now, the program prints its own warning if length of an output sequence name is too long for "pretty" GenBank representation, according to GenBank standard (Dec 15, 2018) 229.0. In previous versions of the program, BioPython warning used to be emitted, which is not very informative: "Increasing length of locus line to allow long name. This will result in fields that are not in usual positions.".

2023-05-25 edition

Version 3.0.b

Fix a bug preventing con-hi from parsing samtools version output correctly if samtools is compiled with a flag -ffile-prefix-map. In that case, the samtools version output contains some non-utf8 characters.

2022-07-26 edition

Version 3.0.a

  1. Add option -l/min-feature-len. It sets minimum length of an output feature.

  2. Add option -C/upper-coverage-coefficients. It sets threshold(s) for annotating high-coverage regions. For example, to annotate regions with coverage > 1.7×M, where M is median coverage, you should specify -C 1.7. You can specify multiple coefficients: -C 1.5,1.7, in the same way as for option -c.

  3. Change long option name: -c/coverage-thresholds -> -c/lower-coverage-thresholds.

  4. Options -c and -C can be disabled now: specify -c off, -C off, and low-coverage or high-coverage regions won't be annotated, respectively.

  5. Add option -k/--keep-temp-cov-file. If it is specified, temporary file coverages.tsv won't be deleted after work of the program.

2022-04-26 edition

Version 2.3.a

  1. Add recommendation "samtools 1.13 or later is recommended". This is the version, in which samtools depth had beed completely rewritten. Since 1.13, samtools depth calculates coverage more accurately.

  2. Now con-hi does not crash if samtools version is of the following format: 1.15.1 (three dot-separated numbers). Previously, only two dot-separated numbers were permitted.

2022-02-23 edition

Version 2.2.b

Changes:

  1. Now con-hi removes its temporary file coverages.tsv, where coverage value of each base is stored.
  2. A bug was fixed that would cause the program to write error message about an unmet dependency to stout instead of stderr.

2022-02-10 edition

Version 2.2.a

Now con-hi adds a comment to output GenBank files. Here is the example of such a comment:

COMMENT     ##Coverage-Data-START##
            Minimum Coverage    :: 0
            Average Coverage    :: 147.54
            Median Coverage     :: 70
            Maximum Coverage    :: 2009
            Zero-coverage bases :: 278 bp
            ##Coverage-Data-END##

2022-01-24 edition

Version 2.1.a

Now con-hi is compatible with samtools 1.13+.

2021-12-23 edition

Version 2.0.b

Now con-hi calculates and prints average coverage.

2021-12-09 edition

Version 2.0.a

Removed options -o/--outdir and --prefix.

Added option -o/--outfile. And now con-hi.py writes all GenBank output records to this single output GenBank file.

2021-06-15 edition

Version 1.1.a

con-hi no more piles up coverage features with identical locations. It means that you will not see both "zero coverage" and "coverage < 10" features starting at the same positions and ending at the same positions.

2021-06-11 edition

Version 1.0.d

Added warning messages for following cases:

  1. If the program cannot find ids of sequence(s) from -f fasta file in the coverage file.
  2. If length of sequence in -f fasta file is not equal to number of coverage positions reported by samtools depth and stored in the coverage file.

2021-06-10 edition

Version 1.0.b

Fixed bug that would cause the program to stumble on a non-extant directory in PATH while checking dependencies.

And then...

Version 1.0.c

Fixed bug that cause the program to stumble on lowercase input sequences.

2021-06-03 edition

Init release. Version 1.0.a