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It seems `Jasmine` does not support `vcf.gz` or `bcf` files:
```
Warning: input.vcf.gz ends with .gz, but (b)gzipped VCFs are not accepted
Exception in thread "main" java.lang.Exception: input.vcf.…
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In BCF, the Character/String type does not have MISSING or EOV encoding given in the spec. htslib and GenomicsDB define MISSING and EOV for String/Character to be `0x07` and `0x00` respectively, but h…
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Dear Tobias,
I am presently executing the somatic structural variant (SV) calling pipeline on data from 173 patients. I've observed that processing one sample typically requires around two days. Th…
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I want to get a feel for the library, but can't follow along w the docs because I don't have dummy data.
```python
>>> from pysam import VariantFile
>>>
>>>
>>> bcf_in = VariantFile("test.bcf…
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`BCF2Codec` has not been well-maintained over the years, and does not fully support the latest BCF 2.2 spec (see the BCF section in http://samtools.github.io/hts-specs/VCFv4.3.pdf). We now have at lea…
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Hello,
We have a multisample bcf which was generated from a heterogenous exome data pool.
To generate the PED and MAP file, we used the command -
`time plink --bcf all_samples.bcf --recode ta…
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It would go something like this:
```yaml
bcf_list:
id: TEST-Biallelic-SNPS-5-fish-maf-0.1
path: .test/bcf/test.bcf
sample_subset_path: .test/config/sample_subsets/fish5.txt…
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CompileC /Users/leon/Library/Developer/Xcode/DerivedData/QPatch-gvmpfbziiefwslesfbaeoapqwxkb/Build/Intermediates/QPatch.build/Debug-iphoneos/QPatch.build/Objects-normal/armv7/QTradeStart.o QPatch/Patc…
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TestFile:
main.m:
```
#import
#import "TestClass.h"
int main() {
@autoreleasepool {
// insert code here...
NSLog(@"Hello, World!");
TestClass *tst = [[TestCla…