Convert alleleCounter c from samtools to use htslib exclusively #10
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Sync with master
additional boiler plate should additional years be added
…w converted to use htslib and work for both bam and cram
…ntirely. Now supports bam and cram inputs
Changed ref-file to say it needs a fasta index
ghost
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Fixes #9
No longer requires samtools for compilation
Supports cram and bam formats
Will require up to date htslib (>= 1.2)