counts: reporting chromosomes without mapped reads #118
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… mapping to them. Ensuring the order of chromosomes is the same as in the header of the SAM file. Adding option to report progress but verbose default does not report for every chromosome. Verifying that chromosome names and sizes are identical in the reference genome and the SAM file header.
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Ensuring that all chromosomes are reported even if some have no reads mapping to them. Ensuring the order of chromosomes is the same as in the header of the SAM file. Adding option to report progress but verbose default does not report for every chromosome. Verifying that chromosome names and sizes are identical in the reference genome and the SAM file header.