v.0.3.1

What's Changed

Bug fix for the bam stats that were not correct for bam files with multiple references (ref, mapped reads)

• Fix stats by @jonas-fuchs in #20

Full Changelog: v.0.3...v.0.3.1

v.0.3

What's Changed

Now stats from the title are dumped to a tabular file. Additionally smaller bugs were fixed.

How recovery and coverage are calculated:

• recovery: percent of position with at least min-cov within a given genomic range.
• coverage: just the mean over the genomic range

PR: Dump bam stats by @jonas-fuchs in #18

Full Changelog: v.0.2.4...v.0.3

v.0.2.4

FIXES:

Fixed a bug where the ABOBEC activity prediction would fail if the variant is located at the genome end

v.0.2.3

FIXES:
Small fix for the mean coverage calculation. Previously calculations were wrong if regions fell under the coverage cutoff due to how the df was subset.

v.0.2.2

NEW
added -q argument that allows a custom bam quality threshold (prior the threshold was 15)

FIXES
fixed the -v argument

v.0.2.1

NEW

• added assessment if mutation could have been caused by APOBEC

FIXED

• fix crash if bed file had no strand information

v.0.2

NEW

• full SNP and INDEL annotation if they lie in a CDS
• bin size for coverage plot

v.0.1.2

FIXES

• fixed a bug that did not plot the track if no vcf and gb were provided
• moved requirement locations

v.0.1.1

v.0.1 HOTFIX

FIXES

vcf annotation:

• correct point mutation types
• now looks for multiple cds identifying tags for vcf annotation
• correct amino acid

visual:

• small visual bug fix for vcf track

v.0.1

Happy for this first alpha version of BAMdash. Included quite a lot of stuff:

• interactive coverage plots
• interactive track plots
• additional hover information
• stat calculation from coverage data
• vcf annotation from gb files
• buttons for coverage y axis
• dark mode mode
• annotated track information to files