3,045
edits
Changes
From Genome Analysis Wiki
Jump to navigationJump to searchno edit summary
* [[C++ Executable: bam#splitChromosome|splitChromosome - Split BAM by Chromosome]]
* [[C++ Executable: bam#splitChromosome|splitChromosome - Split BAM by Chromosome]]
* [[C++ Executable: bam#writeRegion|writeRegion - Write the alignments in the indexed BAM file that fall into the specified region]]
* [[C++ Executable: bam#writeRegion|writeRegion - Write the alignments in the indexed BAM file that fall into the specified region]]
* [[C++ Executable: bam#dumpRefInfo|dumpRefInfo - Print SAM/BAM Reference Information]]
* [[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 22 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 22 and write it out as a SAM/BAM file]]
Wrote t.sam with 2 records.
Wrote t.sam with 2 records.
</pre>
</pre>
== dumpRefInfo ==
The <code>dumpRefInfo</code> option on the bam executable prints the SAM/BAM file's reference information.
=== Parameters ===
<pre>
Required Parameters:
--in : the SAM/BAM file to be read
Optional Parameters:
--noeof : do not expect an EOF block on a bam file.
--printRecordRefs : print the reference information for the records in the file (grouped by reference).
</pre>
=== Usage ===
./bam dumpRefInfo --in <inputFilename> [--noeof] [--printRecordRefs]
=== Return Value ===
* 0: the file was processed successfully.
* non-0: the file was not processed successfully.
<pre>
<pre>
Required Parameters:
Required Parameters:
--bamIndex : the path/name of the bam index file to display
Optional Parameters:
Optional Parameters:
--refID : the reference ID to read, defaults to print all
--summary : only print a summary - 1 line per reference.
</pre>
</pre>
=== Usage ===
=== Usage ===
./bam dumpIndex <bamIndexFile> <ref#>
./bam dumpIndex --bamIndex <bamIndexFile> [--refID <ref#>] [--summary]
=== Return Value ===
=== Return Value ===
* -1 if the bam index file could not be opened.
* 0: the BAM index file was processed successfully.
* 0 if the bam index file could be opened.
* non-0: the BAM index file was not processed successfully.
