Comments (7)
is this for whole genome? can you share a single crai file that has this problem?
from goleft.
It's more complicated than I thought. Sent you two crai files (via funet filesender, you should have the email), one good, one bad.
from goleft.
I see what you mean about scaling.
goleft indexcov -d /tmp/tt --fai /data/human/g1k_v37_decoy.fa.fai ~/Downloads/bad.cram.crai
on the bad.cram.crai that you sent. I will look into this. For #37, could you send a bam for that as well?
from goleft.
I have found a fix for this. There was a problem with the calculation of median depth for scaling to 1 that only manifested in extreme cases like yours.
Would you try the attached binary and confirm that this resolves it for you?
thanks for reporting.
from goleft.
Now all crams work but almost all bams don't. Only 2 out of 119 have median value > 10^-5.
from goleft.
I fixed a bug that I introduced during that change and neglected to update the binary here. would you mind trying this one?
goleft.gz
from goleft.
please re-open if the problem persists with latest version.
from goleft.
Related Issues (20)
- Differential header stringency depending on file format HOT 4
- goleft depth sliding window analysis HOT 1
- Feature request: New option --exclude for indexsplit HOT 1
- indexcov support for csi indexes HOT 2
- ndexcv: excluding chromosome: NC_031965 because of exclude-pattern: ^chrEBV$|^NC|_random$|Un_|^HLA\-|_alt$|hap\d HOT 2
- goleft_linux64 covstats error: panic: EOF HOT 7
- coverage of the customized genome HOT 2
- error: bam is required HOT 4
- link to golang typo
- suggestion: zoomable chromosome depth plots in indexcov HOT 1
- indexcov shows stepwise coverage distribution HOT 4
- Feature request: New option --exclude for covstats HOT 2
- Indexcov errors HOT 2
- error on depth, seems to make temp file it can't find
- Negative alnSpan error HOT 2
- No longer possible to build from source or include in a Docker image HOT 2
- Running Indexcov on cram files with different paths HOT 2
- What is the value of the insert size ? HOT 2
- indexcov: usage with long reads ? HOT 1
- Indexcov searching for cram.bai HOT 1
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from goleft.