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* [[C++ Executable: bam#dumpIndex|dumpIndex - Dump a BAM index file into an easy to read text version]]
* [[C++ Executable: bam#dumpIndex|dumpIndex - Dump a BAM index file into an easy to read text version]]
* [[C++ Executable: bam#readIndexedBam|readIndexedBam - Read an indexed BAM file reference by reference id -1 to the max reference id and write it out as a SAM/BAM file]]
* [[C++ Executable: bam#readIndexedBam|readIndexedBam - Read an indexed BAM file reference by reference id -1 to the max reference id and write it out as a SAM/BAM file]]
* [[C++ Executable: bam#filter|filter - ]]
* [[C++ Executable: bam#filter|filter - Filter reads by clipping ends with too high of a mismatch percentage and by marking reads unmapped if the quality of mismatches is too high]]
* [[C++ Executable: bam#readReference|readReference - ]]
* [[C++ Executable: bam#readReference|readReference - Print the reference string for the specified region]]
This executable is built using the [[C++ Library: bam|bam library]].
This executable is built using the [[C++ Library: bam|bam library]].
=== Return Value ===
=== Return Value ===
* 0
* 0
== filter ==
The <code>filter</code> option on the bam executable filters the reads in a a SAM/BAM file. This option is documented at: [[Bam Executable: Filter]]
== readReference ==
The <code>readReference</code> option on the bam executable prints the specified region of the reference sequence in an easy to read format.
=== Parameters ===
<pre>
Required Parameters:
--refFile : the path/name of the reference file
Optional Parameters:
--refID : the reference ID to read, defaults to print all
--summary : only print a summary - 1 line per reference.
</pre>
=== Usage ===
./bam readReference --refFile <referenceFilename> --start <0 based start> --end <0 based end>|--numBases <number of bases>
=== Return Value ===
* 0: the reference file was successfully read.
* non-0: the reference file was not successfully read.
