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BamUtil

1,777 bytes added, 15:39, 30 June 2010
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Number of records = 10
Returning: 0 (SUCCESS)
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== writeRegion ==
 
The <code>writeRegion</code> option on the bam executable writes the alignments in the indexed BAM file that fall into the specified region (reference id and start/end position).
 
=== Parameters ===
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Required Parameters:
--in : the BAM file to be read
--out : the SAM/BAM file to write to
Optional Parameters:
--noeof : do not expect an EOF block on a bam file.
--bamIndex : the path/name of the bam index file
(if not specified, uses the --in value + ".bai")
--refID : the BAM reference ID to read (defaults to -1: unmapped)
--start : the 0-based start position (defaults to -1)
--end : the 0-based end position (defaults to -1: meaning til the end of the reference)
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=== Usage ===
 
./bam writeRegion --in <inputFilename> --out <outputFilename> [--bamIndex <bamIndexFile>] [--noeof]
 
=== Return Value ===
* 0: all records are successfully read and written.
* non-0: at least one record was not successfully read or written.
 
=== Example Output ===
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The following parameters are in effect:
 
Input Parameters
--in [test/testFiles/sortedBam.bam], --out [t.sam], --bamIndex [], --refID,
--start [1], --end [100], --noeof
 
Wrote t.sam with 2 records.
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== dumpIndex ==
The <code>dumpIndex</code> option on the bam executable prints BAM index file in an easy to read format.
 
=== Parameters ===
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Required Parameters:
bamIndexFile - path/name of the index file to display
Optional Parameters:
ref# - the reference number to print (optional) defaults to print all
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=== Usage ===
./bam dumpIndex <bamIndexFile> <ref#>
=== Return Value ===
== readIndexedBam ==
The <code>readIndexedBam</code> option on the bam executable reads an indexed BAM file reference id by reference id -1 to 22 and writes it out as a SAM/BAM file.
 
=== Parameters ===
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Required Parameters:
inputFilename - path/name of the input BAM file
outputFile.sam/bam - path/name of the output file
bamIndexFile - path/name of the BAM index file
Optional Parameters:
ref# - the reference number to print (optional) defaults to print all
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=== Usage ===

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