merge-hits
----------

This script merges read hits generated by running gmapper across several
databases. It works for both sam and shrimp output format.


Parameters:

<out-file1> <out-file2> ...

--dest-file <dest-file>
	This parameter is required. It specifies the file where all hits will be
	stored.

--paired
--unpaired
	These parameters specify whether the hits were generated by running
	gmapper in paired mode (with -p) or not.

--tmp-dir <tmp-dir>
	Specifies a temporary directory to use. Defaults to /tmp/<PID>.

--suffix <suffix>
	Specifies an awk-style regexp matching the ending of a read tag that
	specifies whether the read is the first or second in a pair. This suffix
	is only used when neither --paired nor --unpaired is given, and only if
	shrimp output format is detected (and not sam). Defaults to ":[^:]*$".


Note:
	If neither --paired nor --unpaired is given, a script is run to detect
	the correct setting.
