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Hi,
I've encountered an issue with the R script generated by `VariantRecalibrator` during my analysis. The generated R script uses color functions (`scale_fill_gradient`) where the RGB color space …
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Some exciting news!
The Methods team at Broad recently applied for, and were subsequently awarded a [grant](https://chanzuckerberg.com/eoss/proposals/htsjdk-enhancing-the-java-toolkit-for-emergin…
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`EnaRefServiceTest` is failing in master with a `GaveUpException`:
```
Gradle suite > Gradle test > htsjdk.samtools.cram.ref.EnaRefServiceTest.test FAILED
htsjdk.samtools.cram.ref.EnaRefService$G…
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When I try ./gradlew vcf2bam, it always reports an error
[ant:javac] /lustre/sdb/zhangyaoz/lyr/software/jvarkit/src/main/java/com/github/lindenb/jvarkit/tools/vcf2bam/VcfToBam.java:27: error: canno…
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Hi
extractFragmentsToFastq fail to extract Quality Line for one read from CRAM file.
INFO 2022-04-07 08:09:12 ExtractBestViralReference Identifying best viral reference genomes from…
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Work with project maintainers and stakeholders to create a roadmap document for the next generation of the HTSJDK file-parsing library, and obtain buy-in from all stakeholders.
From our point of vi…
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Based on a GATK test run using a locally built htsjdk, the following are prerequisites to upgrading to the next htsjdk release (post-2.19.0):
- https://github.com/broadinstitute/gatk/issues/5839
-…
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Currently in Hellbender we have:
GenomeLoc
|-->UnvalidatingGenomeLoc
htsjdk has:
Feature (not conceptually an interval, but it's the same interface as an interval and bed features are nothing but…
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Socrates appears to not be creating a required index file correctly. A 0 byte input_short_sc.bai file was created.
```
Running Socrates with the following options:
threads: 9
long-sc-l…
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CountVariants and SelectVariants both read the same file successfully.
gatk-launch SortVcf --input /humgen/test.filtered.maf_annotated.vcf --output sortvcf.vcf
htsjdk.tribble.TribbleException$Malfor…