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brentp / goleft

goleft is a collection of bioinformatics tools distributed under MIT license in a single static binary
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indexcov : won't work with multiple crais #32

Closed javierpradom closed 7 years ago

javierpradom commented 7 years ago

Works fine with a single crai but appears to fail when running multiple crais. Found this error before? ~/src/go/bin/goleft indexcov -d SEQCAP_WGS_GDAP_Uganda/goleft --sex "chrX,chrY" --fai fasta/Homo_sapiens.GRCh38_full_analysis_set_plus_decoy_hla.fa.fai 21601_6.cram.crai 21722_8.cram.crai panic: runtime error: makeslice: cap out of range

goroutine 23 [running]: github.com/brentp/goleft/indexcov/crai.makeSizes(0xc421132f00, 0x1, 0x10, 0xc4204224d8, 0x0, 0x1) /nfs/users/nfs_j/jpm/src/go/src/github.com/brentp/goleft/indexcov/crai/crai.go:64 +0x13d github.com/brentp/goleft/indexcov/crai.(Index).Sizes(0xc4202a5b20, 0xc4201340f0, 0x50, 0x50) /nfs/users/nfs_j/jpm/src/go/src/github.com/brentp/goleft/indexcov/crai/crai.go:48 +0xa6 github.com/brentp/goleft/indexcov.(Index).init(0xc4201340f0) /nfs/users/nfs_j/jpm/src/go/src/github.com/brentp/goleft/indexcov/indexcov.go:80 +0x4cb github.com/brentp/goleft/indexcov.readIndex(0x7ffd139db8b1, 0x33, 0x0, 0x1, 0x0, 0x0, 0x0) /nfs/users/nfs_j/jpm/src/go/src/github.com/brentp/goleft/indexcov/indexcov.go:417 +0x67d github.com/brentp/goleft/indexcov.Main.func1(0xc42012a3c0, 0xc4202a5ae0, 0x2, 0x2, 0xc4201299f0, 0x2, 0x2, 0xc420129a00) /nfs/users/nfs_j/jpm/src/go/src/github.com/brentp/goleft/indexcov/indexcov.go:351 +0xaa created by github.com/brentp/goleft/indexcov.Main /nfs/users/nfs_j/jpm/src/go/src/github.com/brentp/goleft/indexcov/indexcov.go:356 +0x3b9

brentp commented 7 years ago

can you make sure that these are generated with samtools 1.5 or greater? to rule out the previous bug in indexing? if you still see it, then please sent the .crai files and I'll get it sorted.

javierpradom commented 7 years ago

That seems to solve the problem though some crais with the same samtools version seem to work.

brentp commented 7 years ago

yeah, it would be intermittent--not all crai's will have the problematic behavior.

brentp commented 7 years ago

as far as I know, there aren't a lot of people using this with crai's, so you may hit some other issues. Please let me know if you do. thanks for following up.