https://github.com/cbg-ethz/smallgenomeutilities - 0.5.2

Version 0.5.2

bugfixes:

• paired_end_read_merger don't crash on nested reads due to quality issue (heavy quality-timming or aligner soft-clipping) one read can be entirely fit within it's paired mate

• aln2basecnt don't crash on CDC IRMA's .bam with N cigar operators SAMv1: For mRNA-to-genome alignment, an N operation represents an intron. For other types of alignments, the interpretation of N is not defined.

- Python
Published by DrYak about 1 year ago

https://github.com/cbg-ethz/smallgenomeutilities - 0.5.1

Version 0.5.1

features:

• coveragedepthqc directly supports TSV generated by samtools depth and CDC's IRMA

Minor qualitiy-of-life improvement:

• pairedendread_merger better logging and progress bars
• documentation update

- Python
Published by github-actions[bot] about 1 year ago

https://github.com/cbg-ethz/smallgenomeutilities - 0.5.0

Version 0.5.0

New features

• pairedendread_merger merge aligned paired end reads into full amplicon

• coveragedepthqc gives the percentage of the genome that is covered at least at the specified coverage depth

Bug fixes

• frameshiftdeletionschecks remove unexpected columns in TSV report with --no-english

- Python
Published by github-actions[bot] over 1 year ago

https://github.com/cbg-ethz/smallgenomeutilities - 0.4.1

Version 0.4.1

• [bugfix] recent versions of BioPython have deprecated functionality used by frameshiftdeletionschecks (.position, nogap, wrappers)

- Python
Published by github-actions[bot] about 2 years ago

https://github.com/cbg-ethz/smallgenomeutilities - 0.4.0

• frameshiftdeletionschecks: --chain option as alternative to running mafft
• packaging modernized

- Python
Published by github-actions[bot] almost 3 years ago

https://github.com/cbg-ethz/smallgenomeutilities - 0.3.9

Bugfixes:

• frameshiftdeletionschecks: fixes bugs in interactions between stop codons and indels
• aln2basecnt: avoid crashes on empty sequences (e.g.: after primer trimming with samtools)

- Python
Published by DrYak over 3 years ago

https://github.com/cbg-ethz/smallgenomeutilities - 0.3.8

• Multiple bug and deprecation fixes and updates in framshift reporting script
• Increased portability

- Python
Published by mcarrara-bioinfo over 3 years ago

https://github.com/cbg-ethz/smallgenomeutilities - 0.3.7

What's Changed

• Save aligned consensus by @mcarrara-bioinfo in https://github.com/cbg-ethz/smallgenomeutilities/pull/15
• Add stop codons detection and reporting in the frameshiftdeletionscheck script by @mcarrara-bioinfo in https://github.com/cbg-ethz/smallgenomeutilities/pull/16

New Contributors

• @mcarrara-bioinfo made their first contribution in https://github.com/cbg-ethz/smallgenomeutilities/pull/15

Full Changelog: https://github.com/cbg-ethz/smallgenomeutilities/compare/0.3.6...0.3.7

- Python
Published by mcarrara-bioinfo almost 4 years ago