CRAM support added w/samtools. Multithreaded computation is added for…#66
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valeu merged 1 commit intoBoevaLab:masterfrom Oct 14, 2019
Merged
CRAM support added w/samtools. Multithreaded computation is added for…#66valeu merged 1 commit intoBoevaLab:masterfrom
valeu merged 1 commit intoBoevaLab:masterfrom
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… samtools. CRAM for sambamba is disabled as there is a sambamba bug when reading CRAMs.
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Several changes:
1- CRAM support is added when samtools is used. Sambamba is disabled for CRAM, since sambamba uses a very old version of htslib that causes segmentation fault with CRAM files.
2- Sambambathreads now defaults to maxThreads even when samtools is used. The value is passed to samtools for multithreaded decompression (-@ maxThreads).
3- fastaFile in BAF options is used for the reference genome for CRAM decompression.