Harriet Dashnow

covstats supporting cram

10

Any chance of covstats supporting cram format? Unsurprisingly, when I tried I got an error: `$ goleft covstats input.cram` ```coverage insert_mean insert_sd insert_5th insert_95th template_mean template_sd pct_unmapped pct_bad_reads pct_duplicate pct_proper_pair...

covmed overestimates coverage?

4

I've noticed that covmed estimates higher median coverage than other tools. For example for a particular whole genome covmed estimates 33.4, while Picard CollectWgsMetrics estimates 27. I've performed similar calculations...

coverage: RuntimeWarning: invalid value encountered in true_divide

8

I've encountered a divide by zero runtime warning and tracked it back to this line in coverage.py: File ".../miniconda3/envs/longstr/lib/python3.7/site-packages/pyranges/methods/coverage.py", line 69, in _coverage _lengths = _lengths / (ends - starts)...

Hi Simon, Every time I use a new feature of bpipe, I'm trying to put my experience into words to help you with documentation: Splitting input files using wildcards: run...

https://github.com/quinlan-lab/STRling/blob/c727509fafef68ead5d122ec855a606d8dca549f/src/strpkg/call.nim#L57

Abbreviated from emailed bug report: " I'm using STRling with CRAM files from the Human Genome Diversity Project (HGDP-ceph) downloaded from there: https://www.internationalgenome.org/data-portal/population/FrenchHGDP. I indexed the files using samtools index...

These exist because the locus was not called in that sample. Should not be reported by default.

0-length intervals occur in output and are invalid bed format - should be 1bp intervals

conda install error message (still installs)

1

conda reports the following error, but still installs just fine. Not sure if this can/should be fixed? Might make users think install has failed. ``` $ conda update -n base...