search

BoevaLab / FREEC

Control-FREEC: Copy number and genotype annotation in whole genome and whole exome sequencing data
147 stars 49 forks source link

CRAM support added w/samtools. Multithreaded computation is added for… #66

Closed calkan closed 4 years ago

calkan commented 4 years ago

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.