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Apparently, the release tarball was generated in such a way that the user who extracts it has no read/execute permissions on the top-level source directory: http://hydra.cryp.to/build/781946/log/raw.
…
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when I run velocyto like this:
>```r
>velocyto run -b /home/shijian/scvelo1/ESCA-5-post-T_.tsv -m /home/shijian/scvelo/human_rmsk.gtf /WFDATA/yang_res_z/0901cp/ESCA-5-post-T/outs/possorted_genome_ba…
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```
What steps will reproduce the problem?
1. make
2.
3.
What is the expected output? What do you see instead?
g++ -DMAXHITS=100 -DTHREAD -funroll-loops -Lsamtools -Isamtools -O3
-DREAD_144 -c al…
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I was playing with [bgzf](https://github.com/biogo/hts/bgzf) archives and it was fairly easy to use `bgzf.Reader` in `bufio.Reader` so the the archive could be read in chunks. In one pass I would make…
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Hi GSC's developers,
I've been testing GSC for variant compression and noticed a couple of issues regarding multi-threading behavior and compression performance:
**Multi-threading Issue:**
It s…
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```
> make
mpicc -c -Wall -g -DHTSLIB -I/home/demis001/include:/home/demis001/bin/htslib-1.10.2/include:/home/demis001/bin/samtools-1.10 aux.c -o aux.o
aux.c: In function ‘sam_popen’:
aux.c:230:9…
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I have spent a couple of weeks looking at [Spark-BAM](http://www.hammerlab.org/spark-bam) and how we might incorporate the improvements in Hadoop-BAM itself so that ADAM and GATK can take advantage of…
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When using the following command:
```
samtools calmd -b .bam hs37d5.fa | samtools view -h - | pmdtools --deamination --range 10 --UDGhalf -n 10000 > .cpg.range.txt
```
The following error oc…
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Hi,
Thanks for writing this plugin!
I'm having trouble using variants/variantsMD5 on uncompressed VCFs, header seems to work fine.
Is it supported to be supported?
/Felix
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This is a clever solution to get the decompression / compression into a separate process, very helpful little tool. This pattern would work well for a couple additional compression tools that my group…