error: bam is required

[clersdom]

I am trying to run golfeft indexcov and seems to not be finding the bam files. For my data I have only the bam and bai files. I am now testing if it works for the test-data/ provided in GitHub and I have the same issue.

I am running: ./goleft_linux64.dms indexcov --directory test-data/ *.bam

And getting the error: `2019/08/13 11:06:56 ERROR: since no .fai was specified, expected input to be a list of bams 2019/08/13 11:06:56 ERROR: got, e.g. .bam panic: open .bam: no such file or directory

goroutine 1 [running]: github.com/brentp/goleft/indexcov.RefsFromBam(0x7ffd95327ff1, 0x5, 0x0, 0x0, 0xffffffffffffff9c, 0xc0000cdbb8, 0x49d619) /home/brentp/go/src/github.com/brentp/goleft/indexcov/indexcov.go:317 +0x4b6 github.com/brentp/goleft/indexcov.getReferences(0x7ffd95327fe6, 0xa, 0xc0001b2f01) /home/brentp/go/src/github.com/brentp/goleft/indexcov/indexcov.go:338 +0xbe github.com/brentp/goleft/indexcov.Main() /home/brentp/go/src/github.com/brentp/goleft/indexcov/indexcov.go:388 +0x1e6 main.main() /home/brentp/go/src/github.com/brentp/goleft/cmd/goleft/goleft.go:68 +0x179 `

I have also the latest version goleft Version: 0.2.1

Thanks in advance.

[brentp]

there are no bams in that directory. what does ls *.bam show in the directory where you ran the command?

[clersdom]

cd test-data/

ls *.bam sample_issue_27_0001.bam

To clarify, I am running Indexcov in a directory that contains the folder test-data/ with the bam sample_issue_27_0001.bam

[brentp]

then instead of ./goleft_linux64.dms indexcov --directory test-data/ *.bam you need to run:

./goleft_linux64.dms indexcov --directory test-data/ test-data/*.bam

[clersdom]

Great, it is working now. I thought the directory was already specifying where the .bam files are. Thanks for the fast help!