Give vg surject opinions about paired-end input - #5021
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Changelog Entry
To be copied to the draft changelog by merger:
vg surjectnow requires either-i/--interleavedor-U/--force-unpairedif it thinks the input smells like paired-end data.vg giraffenow uses the GAM fragment length distribution built-in field, likevg map, instead of a"fragment_length_distribution"annotation.Description
This should help with #4563 by making it impossible to accidentally surject paired-end reads as single-ended, and by warning the user if the default unlimited fragment length limit is used.
This will not help you if you forget to map your reads as paired-end, because it specifically doesn't check for things like
/1and/2in your read names, but we expect users to be wise to that subtlety already if they have experience with linear-reference mapping tools. If we want to complain about mapping reads wrong, we should separately add that check to the mappers.