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BAM store needs support for .csi indexes #926
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Hello, I am working with Barley which have very large chromosomes. Could you please suggest a way in which I could visualize the alignments in JBrowse and still bypass the issue with indices. Thank you. |
.csi
indexes
.csi
indexes
FYI: https://samtools.github.io/hts-specs/SAMv1.pdf
|
FYI, csi also applies to files that have traditionally used tabix indexing
|
Hello Large VCF files need also to be indexed using CSI index, so JBrowse cannot handle them right now. |
Began some basic csi (for vcf currently) parsing here https://github.com/GMOD/jbrowse/tree/csi_index |
Got CSI working for BAM now also :) woo |
Oh man...I almost wet myself with excitement! I want to test this out ASAP with wheat! :) 1 happy man at this prospect! |
... do I dare say that they are currently discussing/adding https://github.com/samtools/hts-specs/pull/321 (will help solve the "guessing" about chunks) |
Oh wow haha. Is that an official solution to "bam index index"? |
I'm pretty sure that it doesn't but it's worth being aware that
*.csi
indexes will replace*.bai
eventually, even for*.bam
files.samtools/hts-specs#240 (comment)
I'm not aware of any progress on migration htslib based parsing of
bam/cram
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