Features

• Added possibility to circumvent --plotgroups limit of 8 by specifying colours.txt manually.
• Added Dockerfile

Release v1.1

• Fixed bugs
• Added dependencies: pysam, tqdm, pyyaml
• Removed dependency: samtools
• Added faster coverage estimation
  • BAM files must be sorted/indexed
• Please report issues if this breaks existing pipelines

• Removed redundant example files
• Fix to view to work with legacy BlobDBs from older versions of BlobTools which did not have read-coverage

• major release

• added unmapped flag when providing no --exclude/--include to get InIn/InUn and UnUn reads
• removed progress flag as it didn't impact performance

• Fixed problems with older versions of samtools which caused crashes due to missing "secondary reads" count in output.
• Fixed false warnings when parsing samtools flagstat output (has no effect on final output)

• bugfixes

New feature

bamfilter : reads from a BAM file get filtered into different files: - *InIn* : both reads of a pair are mapped to a contig in "include" - *InUn*: One read of pair maps to contig in "include", the other is unmapped - *UnUn*: both reads of a pair are unmapped if list of contigs to "include"/"exclude" is supplied, additional files get created: - *ExEx*: both reads of a pair are mapped to a contig in "exclude" - *ExIn* : One read of pair maps to contig in "include", the other maps to contig in "exclude" - *ExUn*: One read of pair maps to contig in "exclude", the other is unmapped

• hotfixes

• fixed behaviour so that no readcovplot is written when plotObj.cov_libs_total_reads_dict[cov_lib] == 0