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, 13:43, 6 April 2010
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| * [[C++ Executable: bam#Read and Validate a SAM/BAM file|Read and Validate a SAM/BAM file]] | | * [[C++ Executable: bam#Read and Validate a SAM/BAM file|Read and Validate a SAM/BAM file]] |
| * [[C++ Executable: bam#Read a SAM/BAM file and write as a SAM/BAM file|Read a SAM/BAM file and write as a SAM/BAM file]] | | * [[C++ Executable: bam#Read a SAM/BAM file and write as a SAM/BAM file|Read a SAM/BAM file and write as a SAM/BAM file]] |
− | * [[C++ Executable: bam#Dump a BAM index file into an easy to read text version. | + | * [[C++ Executable: bam#Dump a BAM index file|Dump a BAM index file into an easy to read text version]] |
− | * [[C++ Executable: bam#Read an indexed BAM file reference by reference id -1 to 22 and write it out as a SAM/BAM file. | + | * [[C++ Executable: bam#Read & Write indexed BAM file|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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| * non-0: at least one record was not successfully read, not valid, or not properly sorted. | | * non-0: at least one record was not successfully read, not valid, or not properly sorted. |
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| + | |
| + | === Example Output === |
| + | |
| + | |
| + | == Read a SAM/BAM file and write as a SAM/BAM file == |
| + | |
| + | === Usage === |
| + | ./bam <inputFile> <outputFile.sam/bam> |
| + | |
| + | === Return Value === |
| + | |
| + | |
| + | === Example Output === |
| + | |
| + | |
| + | == Dump a BAM index file == |
| + | |
| + | === Usage === |
| + | ./bam dump_index <bamIndexFile> |
| + | |
| + | === Return Value === |
| + | * -1 if the bam index file could not be opened. |
| + | * 0 if the bam index file could be opened. |
| + | |
| + | === Example Output === |
| + | |
| + | |
| + | == Read & Write indexed BAM file == |
| + | |
| + | === Usage === |
| + | ./bam read_indexed_bam <inputFilename> <outputFile.sam/bam> <bamIndexFile> |
| + | |
| + | === Return Value === |
| + | * 0 |
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| === Example Output === | | === Example Output === |