Confusing error when input is unmapped

[keiranmraine]

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:

alleleCount/c/src/alleleCounter.c

Line 448 in b2158f0

check(ret==0,"Error retrieving stats from bam file for position %s:%d",locis[j]->chr,locis[j]->pos);

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.