I was wondering if vyellappa's query was resolved? I'm getting the exact same error when I run another program that calls samtools.
Thanks!
Traceback (most recent call last):
File "../conifer/conifer_v0.2/conifer.py", line 597, in <module>
args.func(args)
File "../conifer/conifer_v0.2/conifer.py", line 526, in CF_bam2RPKM
iter = f.fetch(p_chr,p_start,p_stop)
File "csamtools.pyx", line 771, in csamtools.Samfile.fetch (pysam/csamtools.c:8233)
File "csamtools.pyx", line 702, in csamtools.Samfile._parseRegion (pysam/csamtools.c:7458)
ValueError: invalid reference `chr1`
File "../conifer/conifer_v0.2/conifer.py", line 597, in <module>
args.func(args)
File "../conifer/conifer_v0.2/conifer.py", line 526, in CF_bam2RPKM
iter = f.fetch(p_chr,p_start,p_stop)
File "csamtools.pyx", line 771, in csamtools.Samfile.fetch (pysam/csamtools.c:8233)
File "csamtools.pyx", line 702, in csamtools.Samfile._parseRegion (pysam/csamtools.c:7458)
ValueError: invalid reference `chr1`
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