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ccgd-profile / BreaKmer

A method to identify structural variation from sequencing data in target regions
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Mate not found! #7

Open ryanabo opened 9 years ago

ryanabo commented 9 years ago

File "/data/share/Software/software/BreaKmer-master/breakmer.py", line 104, in r.run(tic) File "/data/share/Software/software/BreaKmer-master/sv_processor.py", line 195, in run if not trgt.get_sv_reads() : File "/data/share/Software/software/BreaKmer-master/sv_processor.py", line 468, in get_sv_reads self.extract_bam_reads('sv') File "/data/share/Software/software/BreaKmer-master/sv_processor.py", line 506, in extract_bam_reads pair_indices, valid_reads = process_reads(areads, read_d, bamfile) File "/data/share/Software/software/BreaKmer-master/sv_processor.py", line 32, in process_reads add_discordant_pe(aread, read_d, bamfile) # File "/data/share/Software/software/BreaKmer-master/sv_processor.py", line 65, in add_discordant_pe mate_read = bamfile.mate(aread) File "csamtools.pyx", line 1011, in pysam.csamtools.Samfile.mate (pysam/csamtools.c:11048) ValueError: mate not found

the version of python and pysam: Python 2.7.9 ,pysam-0.7.5