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cortes-ciriano-lab / SComatic

A tool for detecting somatic variants in single cell data
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start > stop #60

Closed xuxif closed 2 months ago

xuxif commented 3 months ago

Traceback (most recent call last): File "/home/xuxf/bin/SComatic-main//scripts/SitesPerCell/SitesPerCell.py", line 369, in main() File "/home/xuxf/bin/SComatic-main//scripts/SitesPerCell/SitesPerCell.py", line 358, in main collect_result(run_interval(row, DICT_sites[row], BAM, FASTA, MIN_COV, MIN_CC, tmp_dir, MIN_BQ, MIN_MQ)) File "/home/xuxf/bin/SComatic-main//scripts/SitesPerCell/SitesPerCell.py", line 131, in run_interval i = bam.pileup(CHROM, START, END, min_base_quality = BQ, min_mapping_quality = MQ, ignore_overlaps = False) File "pysam/libcalignmentfile.pyx", line 1326, in pysam.libcalignmentfile.AlignmentFile.pileup File "pysam/libchtslib.pyx", line 688, in pysam.libchtslib.HTSFile.parse_region ValueError: invalid coordinates: start (248838337) > stop (140010)

Francesc-Muyas commented 2 months ago

Dear user, Thanks for bringing this up. I think I fixed the problem and edited the script accordingly. Could you pull the repo and check the script again?

Thanks, Fran