Comments (2)
I would ask for more clarity around the statement "returns an object with various collected metrics". Is this object already created, is this proposed, what is the definition (or is that the task)? Like you said, it could overlap with the SamFileValidator
.
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After talking to several people, I'm no longer convinced that this should be moved to HTSJDK. It has a fairly rudimentary view of whether two SAMRecords are "equal", and seems more useful as a quick command line "diff"-style tool. Let's close this issue for now.
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Related Issues (20)
- EdgeReadIterator (used in Picard's CollectWgsMetrics) doesn't handle intervals correctly HOT 2
- IntervalTree.Node's methods have package visibility only HOT 1
- What is the non-deprecated replacement for acceptableAlleleBases? HOT 4
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- CRAM files have zero-length blocks with a compression method associated with them (so cannot be decompressed). HOT 1
- VCF sorting change breaks existing VCFs HOT 1
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- Add a better error message when the reference is too long for indexing HOT 5
- Question: Tabix index to find min(POS) and max(POS) in each contig
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- SamReader slower than expected on network drive HOT 1
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- Error when reading a VCF 4.3 file with spaces in INFO field values HOT 1
- htsjdk.samtools.util.IOUtil.assertFileIsWritable on certain NFS environments fails to correctly assess permissions HOT 1
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