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samtools / htsjdk

A Java API for high-throughput sequencing data (HTS) formats.
http://samtools.github.io/htsjdk/
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Add CRAM multi-ref slice index query tests #1343

Closed cmnbroad closed 2 years ago

cmnbroad commented 5 years ago

Most of the CRAM index tests use containers that consist of a single, multi-ref slice (created by providing fewer than the minimum number of records/container - which is defined by CRAMContainerStreamWriter.MIN_SINGLE_REF_RECORDS - but which span multiple reference sequences). Most of the test queries only resolve to the first reference in the series though; we need to add query tests (bai and crai) against a container with a multi-ref slice that resolve to the borders of the individual references in the slice to ensure the correct records are returned.

cmnbroad commented 4 years ago

Fixed in refactoring branch.

cmnbroad commented 2 years ago

Closing as fixed (see CRAMIndexPermutationsTests, which tests both CRAI and BAI index queries against CRAMs that were created with artificially small records-per-slice and minimum-single-reference-slice size values that result in multi-ref containers.