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BamUtil

832 bytes added, 16:17, 28 July 2010
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* [[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#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#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.
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== dumpRefInfo ==
The <code>dumpRefInfo</code> option on the bam executable prints the SAM/BAM file's reference information.
 
=== Parameters ===
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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).
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=== Usage ===
./bam dumpRefInfo --in <inputFilename> [--noeof] [--printRecordRefs]
 
=== Return Value ===
* 0: the file was processed successfully.
* non-0: the file was not processed successfully.
<pre>
Required Parameters:
bamIndexFile - -bamIndex : the path/name of the bam index file to display
Optional Parameters:
ref# - -refID : the reference number ID to print (optional) read, defaults to print all --summary : only print a summary - 1 line per reference.
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=== Usage ===
./bam dumpIndex --bamIndex <bamIndexFile> [--refID <ref#>] [--summary]
=== Return Value ===
* -1 if 0: the bam BAM index file could not be openedwas processed successfully.* non-0 if : the bam BAM index file could be openedwas not processed successfully.

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