mappings-top-hits
--------

This script is used to filter alignments after they have been initially merged.

Parameters:

[--strata] [--sam-unaligned] [--paired] [--half-paired] [--max-alignments] [-o/--report 10] input_filename

<input_filename>
	Merged and readname sorted SAM input. '-' for STDIN.

--strata
	Only report highest scoring alignments for each read.

--sam-unaligned
	Report alignments for reads that are considered unaligned under current settings.

--paired
	Alignments are paired.

--half-paired
	Alignments are paired and half-paired.

--max-alignments <max-alignments>
	Do not not report alignments for reads with more then this many valid alignments under
	the current settings. Default 0, report all.

-o/--report <num-outputs>
	Report at most this many alignments per read. If there are more, select the first seen.
	Default 10.

Output:
	To STDOUT.

