Comments (4)
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.
from goleft.
That seems to solve the problem though some crais with the same samtools version seem to work.
from goleft.
yeah, it would be intermittent--not all crai's will have the problematic behavior.
from goleft.
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.
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.