Releases | Open Source Science

covtobed - Claude update

Breaking Changes ⚠️

Default behavior for invalid alignments has changed: - Previous versions: Invalid alignments (duplicates, failed QC, non-primary, supplementary) were kept by default, but was possible to skip them with --discard-invalid-alignments - v1.4.0: Invalid alignments are now discarded by default for cleaner coverage analysis

New Features

--keep-invalid-alignments: Restore legacy behavior to include invalid alignments in coverage calculation
--discard-invalid-alignments: Still valid but does not change the behaviour
Better handling of edge cases in alignment processing
Expanded test suite (integration)
CMake and Unit Tests

If your pipeline depends on the previous behaviour of including invalid alignments:

```bash # Old command (v1.3.x and earlier): covtobed input.bam > output.bed

# New equivalent command (v1.4.0+): covtobed --keep-invalid-alignments input.bam > output.bed ``` For new workflows, the default behavior provides cleaner coverage tracks by excluding low-quality alignments.

Technical Details

Invalid alignments include: - Duplicate reads (SAM flag 0x400) - Failed quality control (SAM flag 0x200) - Non-primary alignments (SAM flag 0x100) - Supplementary alignments (SAM flag 0x800)

Scientific Software - Peer-reviewed - Makefile
Published by telatin 8 months ago

covtobed - v1.3.5

Simpler input sorted check

Scientific Software - Peer-reviewed - Makefile
Published by telatin about 4 years ago

covtobed - v1.3.3

Introduced a sortedness check

Scientific Software - Peer-reviewed - Makefile
Published by telatin about 4 years ago

covtobed - v1.3.1 bugfix

Fixed #12 When splitting the output by strand, if the coverage was not changing this resulted in inconsistent results.
Added a check #13

Scientific Software - Peer-reviewed - Makefile
Published by telatin over 4 years ago

covtobed - v1.3.0 - Quiet mode

When invoked without arguments, covtobed will print a message to inform the user that it is waiting for input from STDIN.

To suppress this message, set the environment variable COVTOBED_QUIET to 1.

Scientific Software - Peer-reviewed - Makefile
Published by telatin over 4 years ago

covtobed - v1.2.0 - Skip short chromosomes

Scientific Software - Peer-reviewed - Makefile
Published by telatin over 5 years ago

covtobed - v1.1.4 - Physical coverage

Will warn to use samtools fixmate when physical coverage calculations result in unexpected coverage after the end of a contig. (#11)

Scientific Software - Peer-reviewed - Makefile
Published by telatin over 5 years ago

covtobed -

Scientific Software - Peer-reviewed - Makefile
Published by telatin over 5 years ago

covtobed - v1.1.0

This release introduces the -d flag to skip poor quality alignments that are: * With mapping quality of 0 (a more stringent filter can be set) * Duplicate alignments * Non-primary alignments * Failing vendor QC

Minor updates: * When parsing an unsorted BAM it will raise an appropriate error * Expanded test suite * Expanded documentation

Scientific Software - Peer-reviewed - Makefile
Published by telatin almost 6 years ago