indexcov: panic: runtime error: index out of range

[sjackman]

❯❯❯ goleft_linux64 indexcov -d indexcov foo.bam 
2017/05/18 15:33:16 indexcov: running on 1 indexes
(WARNING) indexcov: expected 2 sex chromosomes, found: 0.
you can set the expected with --sex ''
2017/05/18 15:33:17 sex chromosomes not found.
2017/05/18 15:33:17 got: 1 principal components
2017/05/18 15:33:17 indexcov: 1 principal components, not plotting
panic: runtime error: index out of range

goroutine 1 [running]:
github.com/brentp/goleft/indexcov.plotSex(0xc4203f8840, 0xc4201591a0, 0x2, 0x2, 0xc420294600, 0x1, 0x1, 0x0, 0x0, 0x0, ...)
	/home/brentp/go/src/github.com/brentp/goleft/indexcov/plot.go:371 +0xc22
github.com/brentp/goleft/indexcov.writeIndex(0xc4203f8840, 0xc42000c130, 0x1, 0x1, 0xc4201591a0, 0x2, 0x2, 0xc420294600, 0x1, 0x1, ...)
	/home/brentp/go/src/github.com/brentp/goleft/indexcov/indexcov.go:742 +0x1cda
github.com/brentp/goleft/indexcov.Main()
	/home/brentp/go/src/github.com/brentp/goleft/indexcov/indexcov.go:382 +0x8ca
main.main()
	/home/brentp/go/src/github.com/brentp/goleft/cmd/goleft/goleft.go:68 +0x191
❯❯❯ goleft_linux64 --version
goleft Version: 0.1.16

The BAM is of reads mapped to an assembly of those reads. I can send along the BAI file if it helps troubleshooting.

[brentp]

well, that's a regression. yes, the bai would be appreciated.
could you use this: https://github.com/brentp/goleft/releases/download/v0.1.10/anonymize-for-indexcov_linux64
to make a stub bam, bai from your originals?

[sjackman]

The original .bai file is 30 kb. Here it is:
ftp://ftp.bcgsc.ca/public/sjackman/goleft/v4.bam.bai

[brentp]

Thanks.
I am making a fix for this now, but you can also run with --sex '' and it will complete--though your data doesn't look very exciting.

[sjackman]

Thanks, Brent. I'll try it tomorrow.

though your data doesn't look very exciting.

Ouch. Burn.

[sjackman]

The --sex '' workaround worked. Thanks! I'm using the plots to identify large collapsed repeats in a de novo assembly. It's quite useful. Thanks, Brent.

[brentp]

good to hear. thanks for the test-case.