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Add tool_dependencies.xml and test-data
author Jim Johnson <jj@umn.edu>
date Mon, 01 Apr 2013 10:57:16 -0500
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**What it does**

This tool uses the samtools view command in SAMTools toolkit to filter a SAM or BAM file on the MAPQ (mapping quality), FLAG bits, Read Group, Library, or region.

**Input**

Input is either a SAM or BAM file.

**Output**

The output file will be of the same format a the Input file, filtered by the selected options.

**Options**

Filtering by read group or library requires headers in the input SAM or BAM file.

If regions are specified, only alignments overlapping the specified regions will be output.  An alignment may be given multiple times if it is overlapping several regions.
A region can be presented, for example, in the following format

  chr2  (the whole chr2)
  chr2:1000000   (region starting from 1,000,000bp)
  chr2:1,000,000-2,000,000      (region between 1,000,000 and 2,000,000bp including the end points).

Note:  The coordinate is 1-based.

Multiple regions may be specified, separated by a space character

  chr2:1000000-2000000 chr2:1,000,000-2,000,000 chrX