diff README @ 1:f2e4e81f3639

Add tool_dependencies.xml and test-data

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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
+