Support code for NGS copy number algorithms. Takes a file of locations and a [cr|b]am file and generates a count of coverage of each allele [ACGT] at that location (given any filter settings)
This code isn't intended for unmapped BAM files, but logging how it appears.
When an alignment file is not mapped you will see an error similar to this:
[ERROR] (src/bam_access.c: bam_access_get_position_base_counts:454 errno: No such file or directory) Error detected (-2) when trying to iterate through region.
[ERROR] (./src/alleleCounter.c: main:448 errno: None) Error retrieving stats from bam file for position :65885569
The error doesn't print the contig correctly for some reason at this line:
Rather than this being confusing, this should be prevented by checking the header contains @SQ lines and giving an appropriate message if they are absent.
This code isn't intended for unmapped BAM files, but logging how it appears.
When an alignment file is not mapped you will see an error similar to this:
The error doesn't print the contig correctly for some reason at this line:
https://github.com/cancerit/alleleCount/blob/b2158f0a9e7958332674bda0d73fdf39df8a1843/c/src/alleleCounter.c#L448
Rather than this being confusing, this should be prevented by checking the header contains
@SQlines and giving an appropriate message if they are absent.