Release 0.4.0

Release 0.4.0 introduces the following changes to existing tools:

• CallDuplexConsensusReads
  • The single strand consensus bases and quals for each duplex consensus read are output into tags on the duplex consensus read
  • Added option to output consensus reads that are formed from only a single strand
• FilterConsensusReads
  • New option to filter out reads with low mean base quality
  • New option to filter out reads whose minimum depth is too low
  • New option to filter duplex consensus reads where the single strand consensuses disagree
  • New optional tags will store the the single-strand consensus bases and qualities for duplex consensus reads.
• DemuxFastqs
  • will no longer output /1 and /2 on read names when running in Illumina standards mode
  • fixed a bug causing an exception when the sample barcode is found in multiple reads (ex. i5 and i7)
• ErrorRateByReadPosition - fixed bug that resulted in C>G errors being counted as A>G errors
• GroupReadsByUmi
  • Reads with UMIs with Ns in them are now rejected
  • Log messages added with counts of reads filtered out by reason
  • Memory usage improvements when grouping reads at very, very high depth.
  • Supports enforcing a minimum UMI length and partial UMIs except for the paired strategy (duplex sequencing).

Finally, changes to various APIs were as follows:

• Method in Bams to sort records by tag, or by a function applied to a tag
• Improve speed of Metric.read for loading large numbers of rows from metrics files
• Changed SamSource to extend IterableView instead of Iterable so that map(), filter(), etc. return lazy views
• Fixed a bug where the specified temporary directory was not being used for sorting.
• Added a BinomialDistribution class implemented using unlimited precision decimal math which is slower, but allows computation of cumulative probabilities where other implementations overflow or underflow