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, 16:17, 28 July 2010
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| * [[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]] |
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| 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. |
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| <pre> | | <pre> |
| Required Parameters: | | Required Parameters: |
− | bamIndexFile - path/name of the index file to display | + | --bamIndex : the path/name of the bam index file to display |
| Optional Parameters: | | Optional Parameters: |
− | ref# - the reference number to print (optional) defaults to print all | + | --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. |
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