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Is it possible to, all in memory without writing a file, given a list of AlignedSegments and a bam header, build a bam, index and get coverage?

Assuming you are on an operating system that supports them, like Linux, you can try using named pipes in a ramdisk or tmpfs. Not the most elegant approach, but I don't know if what you are asking for ...
terdon's user avatar
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1 vote

Discrepancy in Depth of Coverage Estimation between Pileup and samtools depth

This is purely a guess based on what you write given that you are not showing the exact command for samtools etc. I suspect that you are allowing sequences with MAPQ==0 (supplementary alignments) into ...
Maximilian Press's user avatar

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