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mcmero / SVclone

A computational method for inferring the cancer cell fraction of tumour structural variation from whole-genome sequencing data.
BSD 3-Clause "New" or "Revised" License
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Fetching reads failed #3

Closed glnegri closed 5 years ago

glnegri commented 5 years ago

When I run annotate on the example data I get the following error for all the positions:

-bash-4.2$ python SVclone.py annotate -i example_data/tumour_p80_DEL_svs_simple.txt -b example_data/tumour_p80_DEL_sv_extract_sorted.bam -s example_data --sv_format simple -cfg svclone_test.ini Loading SV calls... Inferring SV directions... Fetching reads failed for loc: 12:227531:227555 Fetching reads failed for loc: 12:228238:228262 Fetching reads failed for loc: 12:333577:333601 Fetching reads failed for loc: 12:338286:338310 Fetching reads failed for loc: 12:461130:461154 Fetching reads failed for loc: 12:465976:466000 ........

mcmero commented 5 years ago

Sorry for the late reply. This is likely caused by newer versions of pysam breaking SVclone's fetching of reads from bam files. This has now been fixed.