-
htslib 1.11 cannot read any files using HTTPS or S3 on macOS. I tested with the following files:
- https://github.com/brentp/cyvcf2/raw/master/cyvcf2/tests/test.vcf.gz
- s3://3kricegenome/test/test.…
-
I tried to install cyvcf2 using pip on my Mac and ran into some issues with cython. It looks like this issue is common as just copy/pasting the cython errors results in a few google hits for other pro…
-
Hi,
I was running Pheniqs the other day on cat'd fastq.gz files from different lanes, great tool! It runs really well until the very end, where it generates an EOF error:
Pheniqs mux --config run…
-
Hi,
I am creating a script to annotate files, and when testing it out I entered an input file. The command I run on that file is: `bcftools annotate -a dict.vcf.gz -c INFO newfile.vcf.gz`
I used…
-
## Bug Report
### Affected tool(s)
picard, CheckIlluminaDirectory
### Affected version(s)
- [ ] Latest public release version [version?]
- [X] Latest development/master branch as of January 2…
-
Right now, `extract_reads` returns only the forward (or reverse) read in a pair of reads if only the forward (or reverse) read contains a kmer in the query nbhd. Is it possible to return both the forw…
-
I have downloaded my Nebula genomics 30X .cram file. I would like to extract the complete list of snps and genotypes resulting in a 23andme style output file. I have successfully installed WGSExtract …
-
I run into a problem with `bcftools reheader`
As I am constructing the new header programmatically , the output file is corrupt if the input VCF file is gzipped or in BCF format (as I stream to stdou…
ghuls updated
3 years ago
-
The code commenting level is poor, functions are too monolithic, np.array functionality is not easily substitutable,
KDB | writer | reader seems clunky.
-
Hi, I installed the Rhtslib and met the error ,could you help me fix this problem , thank you very.
gcc -std=gnu99 -fPIC -I/ds3512/home/panyp/ruanjian/packages/include -fpic -I. -fPIC -I/ds3512/ho…