v3.1.0

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