The pipeline checks that the input bam file is indexed by checking for the .bai extension, which means that indexes .csi are not allowed (although they should be).
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if(not os.path.exists(input + ".bai")): |
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sys.exit("Index supplied .bam before proceeding") |
The pipeline checks that the input bam file is indexed by checking for the
.baiextension, which means that indexes.csiare not allowed (although they should be).bap/bap/cli_bap2.py
Lines 145 to 146 in 44061cd