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Currently alleleCounter throws a trace when it is run on a BAM file that has not been indexed. The trace does not mention the missing index, which would be a helpful message.
The first 2 lines of the error indicate the missing index file:
[ERROR] (src/bam_access.c: bam_access_openhts:55 errno: No such file or directory) HTS index file temp.bam failed to open.
[ERROR] (./src/alleleCounter.c: main:255 errno: None) Error trying to open sequence/index files 'temp.bam'.
Currently alleleCounter throws a trace when it is run on a BAM file that has not been indexed. The trace does not mention the missing index, which would be a helpful message.
Example trace:
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