rasusa

2.1.0 (2024-08-19)

Features

• [aln] add program (@PG) entry to header (0123e54)
• log seed used when --seed not passed (6e1f37d)

2.0.0 (2024-05-03)

⚠ BREAKING CHANGES

• paired reads require --output once for each file

Bug Fixes

• paired reads require --output once for each file (1427a0b)

1.0.0 (2024-04-29)

⚠ BREAKING CHANGES

• move fastq functionality to reads subcommand

Features

• add cite command to get citation (db17612)
• add subcommand aln to subsample alignments (b92979a)
• move fastq functionality to reads subcommand (f48d47b)

Bug Fixes

• deal with chromosomes with no alignments (14aa15e)

0.8.0 (2024-01-03)

Features

• add logging message with coverage of input before downsampling (79445fc)
• support ztsd (cfa50f8)
• use default compression level for compression output type (cfa50f8)

Bug Fixes

• update logging so colour not sent to file (bc62c3f)

0.3.0

Version 0.3.0 may give different results to previous versions. If so,
the differences will likely be a handful of extra reads (possibly none).
The reason for this is --coverage is now treated as a float.
Previously we immediately round coverage down to the nearest integer. As
the number of reads to keep is based on the target total number of
bases, which is coverage * genome size. So if coverage is 10.7 and
genome size is 100, previously our target number of bases would have
been 1000, whereas now, it would be 1070.

Changed

• --coverage is now treated as a f32 instead of being converted
  immediately to an integer #19.
• Updated rust-bio to version 0.31.0. This means rasusa now handles
  wrapped fastq files.
• Preallocate fastx records instead of using iterator. Gives marginal
  speedup.
• Added bash to the docker image b47a8b75943098bdd845b7758cf2eab01ef5a3d8

New

• Support paired Illumina #15