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The SensorML standard states that the Unique Identifier must be a gml:identifier with the codespace "uniqueID" (pg 81). However, there is inconsistency primarily in SensorML examples. For example:
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Hi, is there any way to force chromap to output all the unmapped and multi-mapped reads?
And how are they identified? It was mentioned in issue 20 that multi-mapped reads are assigned mapq=0, how ab…
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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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As has come up in #317 reported by @y9c, when mapping paired-end reads, we should allow for the case that reads overlap in this way:
```
R1 -------->
R2
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It might be interesting to expose an interface that allows users to provide their own functions for splitting files on `put file`.
The use case that I personally have:
Computational biology is …
ghost updated
4 years ago
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*Original issue: https://charm.cs.illinois.edu/redmine/issues/896*
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ICC-15.0+ has a '-fmpc-privatize' option for automatically privatizing static variables. Combined with one of our automatic stra…
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Request:
Add capability to explicitly define alignments (i.e. raw sequence, CIGAR string, quality score, etc) as a json object in the tracks array of the input option object.
Use case:
- display …
LClos updated
2 years ago
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(A) Convert FASTQ to uBAM and add read group information using FastqToSam
Picard's FastqToSam transforms a FASTQ file to an unmapped BAM, requires two read group fields and makes optional specificati…
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The Crypt4GH encrypted file format standard is currently part of the hts-specs repo, where it lives next to the SAM, BAM, CRAM, VCF, BED file format standards: https://github.com/samtools/hts-specs. T…
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I think I get where the modification probabilities are coming from (ML values / 256). But if I pass a filter that's being used for both modified and canonical calls, where does the canonical base prob…