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, 15:01, 30 September 2010
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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]]. |
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| === 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. |