Accurately index outputs from PrintSVEvidence and CollectSVEvidence #9269
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mwalker174
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Oct 1, 2025
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mwalker174
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Thank you @kjaisingh this looks good. I will have another PR that updates the test files with new indexes even though the tests currently pass.
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This PR is intended to accurately index the files output through
PrintSVEvidenceandCollectSVEvidence.Currently, the various codecs accessible through these tools use the column
0as the end column when indexing. However, this is not compatible with later version of htsjdk, so we instead use the column2(which is also the start column) in each of these cases.The
DepthEvidenceCodecis already configured properly, so we do not need to change anything for it.