add option --sam-hit-only #377
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Newly added option --junc-bed was conflicting with my proposed option. I resolved the conflicts. Please consider for merging. The sooner the better so I don't have to do it again :) and can use this option. |
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Hi,
Many downstream tools expect only mapped queries in the SAM output (i.e. accepted hits file). By default, minimap2 output all queries. This request adds the option --sam-hit-only which allows the user to restrict the output to the mapped queries.
Please comment and I would be glad you could consider this request for merging into master. Thanks.
Charles