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.

0.5.1

Version 0.5.1

features:

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

Minor qualitiy-of-life improvement:

• paired_end_read_merger
  better logging and progress bars
• documentation update

0.5.0

Version 0.5.0

New features

• paired_end_read_merger
  merge aligned paired end reads into full amplicon

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

Bug fixes

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

0.4.1

Version 0.4.1

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

0.4.0

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

0.3.9

Bugfixes:

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

0.3.8

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

0.3.7

What's Changed

• Save aligned consensus by @mcarrara-bioinfo in #15
• Add stop codons detection and reporting in the frameshift_deletions_check script by @mcarrara-bioinfo in #16

New Contributors

• @mcarrara-bioinfo made their first contribution in #15

Full Changelog: 0.3.6...0.3.7