fixmate no longer removes PAIRED flag.#2056
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No longer removes paired flag from reads that have no mate (either removed or missing). Fixes samtools#2052 using the idea that the PAIRED flag is a sequencing technology indicator not a feature of alignment.
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Do we need to update the manual page to reflect this change? |
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I think we should, since it is a change in behaviour. |
daviesrob
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May 30, 2024
| Remove secondary and unmapped reads. | ||
| Remove secondary and unmapped reads. If one of a pair is removed, the PAIRED | ||
| flag will not be unset on the remaining read. This is a change from the older | ||
| behaviour. |
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Should probably add something like in samtools versions up to 1.20
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No longer removes paired flag from reads that have no mate (either removed or missing).
Fixes #2052 using the idea that the PAIRED flag is a sequencing technology indicator not a feature of alignment. This is a change in the behaviour of fixmate.