Brad Langhorst

depends on test data in : https://github.com/nf-core/test-datasets/pull/299

-L chr1 runs but does not output anything

1

Thanks for writing this helpful software! I think it should just extract chr1 reads or fail (reporting an invalid -L argument) Using -L chr1:1-248956422 does work

cannot consume -.ubam on a pipe

2

``` samtools view ... | bam trimBam -.ubam -.ubam --clip -R ``` produces this error: ``` bam: invalid option -- '.' ERROR: Unrecognized option left ``` works ok with ```...

The documentation covers the requirement for random ordered input, however It would be nice to add a check to be sure that a bam file is not coordinate sorted before...

noodles implementation is slower than rust-htslib, did I do something suboptimal?

4

rust-htslib: ``` cat 0.00s user 0.01s system 1% cpu 0.568 total sudo cargo run --release -- > tandem_reads.bam 0.43s user 0.04s system 82% cpu 0.570 total ``` noodles: ``` cat...

@dpryan79 This needs more testing, but I wanted to test the waters - is this of use to others?

re #14 I'm running now with this code. It seems to be working (see image) 

In some cases (maybe because this is not a very busy site) requests are issued too quickly and I get this exception: ``` Traceback (most recent call last): File "./google2piwik.py",...

Import .bai files if they are present when importing bam (instead of reindexing)

1

Not a big deal for small bams, but when importing 100G bam files index generation can really slow a workflow.

seg fault

7

I just tried out minimap on a bunch of pacbio reads like this: ``` shell #!/bin/sh PATH="/mnt/home/langhorst/src/miniasm:/mnt/home/langhorst/src/minimap:$PATH" if ! [ -f deer_1123.mmi ]; then minimap -d deer_1123.mmi deer_1123.fasta fi minimap...