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ChangeLog
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ChangeLog
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Added dependabot.yml to auto-update GitHub actions
Updated image labels
[0.18.0]
Updated to handle NanoSeq
Removed the dependency on samtools from the unit tests
[0.17.1]
Add docker tooling and image publishing
[0.17.0]
Change the --nocall-quality option from an integer to boolean, and ensure it applies to QT tags.
[0.16.0]
Fixed bug in read_names caused by overflow of 'float' by changing to 'double'
Added --nocall-quality option for NovaSeqX
Added Acknowledgements file to credit Illumina for test data
[0.15.0]
Initial NovaSeqX support
Fixed memory leak in check_bcl
Make libgd optional
Configuration fixes and improvements
[0.14.0]
new substitution_analysis command
minor changes to handle barcode files containing dual tags with only one tag such as "-ACGT" and "ACGT-"
bcl_check: improved error handling
include BC: tag (barcode) in RG (read group) header lines
[0.13.1]
bug fix: restore default output format to BAM
[0.13.0]
new update command: rewrites querynames in a standard format
output file type will match output file extension (not default to bam)
removed reliance on samtools for tests
[0.12.2]
Uses new htslib header API (htslib >1.9)
i2b option to automatically fix corrupted CBCL blocks
standardise queryname format for NovaSeq (add prefix)
[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)
--rg flag use deprecated but not illegal (functionality removed)
i2b function updated to handle NovaSeq SP flowcell (single surface)
[0.11.2]
integer overflow bug in spatial_filter fixed
[0.11.1]
posix_fadvise() on NovaSeq cbcl files to pre-cache the next tile to speed up reads
bug fix: removeBadTiles() was not being honored 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: decode stats counts templates rather than reads
[0.9.8]
Bug fix: chrsplit function now adds PG lines to output BAM/CRAM header
Bug fix: Handle empty BAM files (bamit)
[0.9.7]
Bug fix: remove old RG lines before adding new ones (decode)
Handle separators in tag indexes
[0.9.6]
decode function refactored to work with read groups instead of individual read records
[0.9.5]
Implemented 'bambi read2tags' for extracting sequence and quality ranges from reads and assigning them to auxiliary tags
[0.9.4]
Implemented 'bambi chrsplit' for SplitBamByChromosome
Implemented 'bambi select' for alignment filtering
Add option to concatenate indexes, optionally with a '-'
[0.9.3]
changes to metrics file output for backwards compatibility (tag#0: no tag name, and perfect_matches pf_perfect matches set to 0)
[0.9.2]
include merge tag function for dual indexes
Bugfix: bam_aux_update_str()
[0.9.1]
i2b - added support for multiple barcode and quality tags
[0.9]
Initial release: implements i2b (converts Illumina files to SAM/BAM/CRAM files) and decode (decode a multiplexed SAM/BAM/CRAM file by read groups)