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@SaberHQ SaberHQ released this 13 Apr 07:04
· 28 commits to master since this release
v3.1.0
23911b6
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This release contains several major bugfixes + new added features as outlined below.

General changes:

  • updated requirements.txt
    • added missing package names (fixes #135)
    • updated package version (fixes #159, #120, and #131)
  • fixed bug where head/tail lengths are calculated without considering the strand of the alignment
  • fixed bug where sequence IDs in _aligned_error_profile do not match those in _aligned_reads.fastq (fixes #151)
  • set default file compression level to 1 (previously level 6)

genome mode:

  • fixes bug where -c option crashes

transcriptome mode:

  • new options for read_analysis.py:
    • -c detect chimeric reads
    • -q quantify transcript expression
    • -n normalize expression values by transcript length
  • new expression quantification algorithm based on abundance estimation in metagenome mode
  • fixed bug where identical read lengths are simulated for the same transcript (fixes #155; thanks Haoran Li)
  • fixed bug where transcripts without a ENS name prefix cannot be simulated, which may result in an infinite loop (fixes #112, #156)
  • optimized various parts of simulation (see #150, #158)
  • fixed bug where head/tail lengths are calculated without considering genome alignments in addition to transcriptome alignments (fixes #136)

metagenome mode:

  • the option --dna_type_list is not required when reference genomes are streamed from RefSeq
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