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quinlan-lab / STRling

Detect novel (and reference) STR expansions from short-read data
MIT License
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Need a more useful error for when bed file chromosomes don't match reference genome #54

Open hdashnow opened 4 years ago

hdashnow commented 4 years ago

strling call -f g1k_v37_decoy.fa -l loci.hg19.bed -o hg002.extra hg002.cram hg002.str.bin

If chromosome names in loci.hg19.bed above don't match the reference genome (e.g. chr 1 vs 1) then the following error occurs:

strling version: 0.1.0 [strling] read format version 0 from software version 0.1.0 [strling] proportion_repeat 0.800 and min mapping quality 40 [strling] reading 843211 STR reads from bin file fatal.nim(39) sysFatal Error: unhandled exception: index -1 not in 0 .. 86 [IndexError] Cleaned up file hg002.extra-bounds.txt to .bpipe/trash/hg002.extra-bounds.txt.1 Cleaned up file hg002.extra-unplaced.txt to .bpipe/trash/hg002.extra-unplaced.txt.1 Cleaned up file hg002.extra-genotype.txt to .bpipe/trash/hg002.extra-genotype.txt.1 ERROR: stage str_call_individual failed: Command in stage str_call_individual failed with exit status = 1 :