cancerit / PCAP-core

NGS reference implementations and helper code for mapping (originally part of ICGC-TCGA-PanCancer)
GNU General Public License v2.0
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support for irods: protocol #53

Open mgcam opened 4 years ago

mgcam commented 4 years ago

bam_stats is unable to read files in iRODS in the presence of iRODS libhts plugin since the check for the file existence in the beginning of the program does not understand irods: protocol. It might be better to leave htslib to figure our whether it can retrieve the file.