0.12.1

bug fix: spatial filter application dumped core when skipping tiles

0.12.0

• multi-threading and optimisations added to decode function
• allow decode option to run in parallel with i2b
• add multiple-lane i2b (merged output)
• spatial_filter handles multi-lanes (multi-lane spatial filter file can be produced)
• new seqchksum function
• use htslib hopen() to enable bambi use with S3, AWS, et al
• check_bcl utility added
• adapter check function added (detect and mark with auxtags, clipping coming soon)
• deprecate --rg flag use (not illegal but functionality removed)
• i2b function updated to handle NovaSeq SP (single surface) flowcell

0.11.1

use posix_fadvise() speed uup reads on NovaSeq cbcl files by pre-caching the next tile
bug fix: bad tile detection restored in spatial_filter application

0.11.0

• fixed divide-by-zero bug in tag hops report
• decode copes with taglist files with empty columns
• spatial_filter supports multiple filter files applied by RG ID
• refactoring of threadpool code and other performance enhancements

0.10.1

tag hops metrics file

• unneeded columns removed
• always create this file if dual index is detected (will only contain header values)

0.10.0

• implemented spatial_filter command
• dual index handling (including tag-hopping report) in decode
• i2b now has multithreading

0.9.12

Bug fix: removed overstringent assertion in select
enhancement: i2b now handles NovaSeq data

0.9.11

Bug fix: decode assigned different read groups to reads in a pair with low quality when --convert-low-quality flag was used

0.9.10

Bug fix: decode memory leak fix

0.9.9

bug fix release: decode stats counts templates rather than reads