[2.5.1] - Bopfingen (Patch) - 2024-02-21

[2.5.1] - 2024-02-21

Added

• #1037 Added an option to deactivate the -sorted option of bedtools coverage, in case the feature file is not sorted the same way as the fasta file, albeit with the caveat this will be very slow. (♥ Thanks to @IdoBar for reporting, and contributing.)

Fixed

• #1048 --vcf2genome_outfile parameter now gets prefixed by the sample_name and suffixed with .fasta (i.e. <sample_name>_<vcf2genome_outfile>.fasta). This ensures we avoid overwriting the output fasta of one sample with that of another when the option is provided. (♥ Thanks to @MeriamOs for reporting.)
• #1047 Changed the row some statistics were reported in the General Stats table. The File name collision fixed in 2.5.0 (see #1017) caused these statistics to be reported in the wrong row due to an added suffix.
• #1051 An error is now thrown if input BAM files end in .unmapped.bam, as this breaks the bam filtering process and empties the bam files in the process. (♥ Thanks to @PCQuilis for reporting.)

Dependencies

Deprecated