Protect against merging CRAM files with different headers.#2220
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The protection of sharing incompatible references between multiple input files aren't strict enough. It was attempting to spot files with reordered references by checking the "lost_coord_sort" flag in the header translation table. However this doesn't cover the case where we are merging completely unrelated files that have no overlap in reference names. Fixes samtools#2218
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The protection of sharing incompatible references between multiple input files aren't strict enough. It was attempting to spot files with reordered references by checking the "lost_coord_sort" flag in the header translation table. However this doesn't cover the case where we are merging completely unrelated files that have no overlap in reference names.
Fixes #2218
Note there may be cases where we can share references for the output file descriptor but we're not doing so. For example if we have two files which are the same references but in different order, then the first and second inputs cannot share a reference as the ordering differs, but by the time we get to writing the translation table has brought them together again so the output could share the reference with the first input.
It's a bit of a corner case though and it's safer to simply avoid optimising the rare case. If any of the input refs can't be shared, we also don't share it to the output. (I think this was another bug in the original design)