hts-nim

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Trouble with newRecord "undeclared identifier" in bam

7

Hi, I'm having trouble initiating new records based on an old Bam file. My goal is to make modifications to certain fields (i.e mapping quality) based on criteria within a...

akkellogg

Get list of INFO and FORMAT keys from Header

1

Hi Brent, Is there a way to get the list of keys for INFO and FORMAT definitions from the header of a VCF using hts-nim? The idea I'm working on...

edg1983

Hello. When I ran `mosdepth` on our bam file I've got error which origin is from `hts-nim` - that's why I've created issue here. Here is my error: ``` root@b79bb970b062:/outputs#...

Stikus

Static binary not working from AMD nodes

6

Hello Brent! I tried compiling a static binary with your docker solution, and it doesn't work from the AMD nodes in the cluster I use. (i.e. the help screen is...

telatin

Closing BGZI gives a 'munmap_chunk(): invalid pointer'

3

Using Nim 2.0.2, hts-nim 0.3.25. (Also, depending of the source, the error is `SIGSEGV: Illegal storage access. (Attempt to read from nil?)`). The minimal example I can do to make...

xbello

Adjust header on load to prevent failing [QUESTION]

1

Hi Brent, I'm wondering if there is a way to manipulate the header while/before opening an uncompressed VCF file to prevent errors and process the file. The use case here...

edg1983