grabix

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incorrect output

11

Hi Aaron, Whilst on the way to getting up to speed on gemini, I've had a play with grabix. Unfortunately it's not playing nicely on our CentOS systems. Following the...

drmjc

Need to a account for headers (e.g., VCF)

1

arq5x

After using this command-$bash master=test.sh. I am getting the following error Using gemini found at: /usr/local/bin/gemini /usr/local/share/gemini/anaconda/lib/python2.7/site-packages/gemini/config.py:61: YAMLLoadWarning: calling yaml.load() without Loader=... is deprecated, as the default Loader is unsafe....

shwetanavle

grabix size returns negative on large file

1

I have a file with 3102468676 lines compressed with pbgzip and indexed with grabix index. grabix size returns -1192498620. It seems that a long int needs to be updated to...

aeschriefer

Hi all, what would it take to enable S3 access in grabix? I was hopeful/naive enough to think that it was as simple as replacing bgzf.c and linking against a...

andreas-wilm

Travis functionality. Consider to squash merge.

mmterpstra

Need BAM support. Can index BAMs in the same way.

1

arq5x

instead of ``` stuff | bgzip -c > o.vcf.gz grabix o.vcf.gz ``` we should have ``` stuff | grabix indexcompress o ```

brentp

``` wget -O - https://github.com/arq5x/gemini/raw/master/test/test.query.vcf | grep ^# | bgzip -c > o.vcf.gz grabix index o.vcf.gz grabix grab o.vcf.gz 1 1 ```

brentp

grabix grab some.vcf.gz 0 returns the same row as grabix grab some.vcf.gz 1

bw2