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, 12:43, 21 May 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#Print SAM/BAM header]] |
| * [[C++ Executable: bam#Dump a BAM index file|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 & 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]] | | * [[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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| This executable is built using the [[C++ Library: bam|bam library]]. | | This executable is built using the [[C++ Library: bam|bam library]]. |
| + | |
| + | Just running ./bam will print the Usage information for the bam executable. |
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| ./bam validate --in <inputFile> [--noeof] [--so_flag|--so_coord|--so_query] [--quitAfterErrorNum <numErrors>] [--maxReportedErrors <numReportedErrors>] | | ./bam validate --in <inputFile> [--noeof] [--so_flag|--so_coord|--so_query] [--quitAfterErrorNum <numErrors>] [--maxReportedErrors <numReportedErrors>] |
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| === Return Value === | | === Return Value === |
| * 0: all records are successfully read, are valid, and are properly sorted. | | * 0: all records are successfully read, are valid, and are properly sorted. |
| * 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 === | | === Example Output === |
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| === Usage === | | === Usage === |
| ./bam <inputFile> <outputFile.sam/bam/ubam (ubam is uncompressed bam)> [NOEOF] | | ./bam <inputFile> <outputFile.sam/bam/ubam (ubam is uncompressed bam)> [NOEOF] |
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| === Return Value === | | === Return Value === |
| Returns the SamStatus for the reads/writes. | | Returns the SamStatus for the reads/writes. |
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| === Example Output === | | === Example Output === |
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| Number of records read = 10 | | Number of records read = 10 |
| Number of records written = 10 | | Number of records written = 10 |
| + | </pre> |
| + | |
| + | |
| + | == Print SAM/BAM header== |
| + | The <code>dump_header</code> option on the bam executable prints the header of the specified SAM/BAM file to cout. |
| + | |
| + | === Parameters === |
| + | <pre> |
| + | Required Parameters: |
| + | filename : the sam/bam filename whose header should be printed. |
| + | </pre> |
| + | |
| + | === Usage === |
| + | |
| + | ./bam dump_header <inputFile> |
| + | |
| + | === Return Value === |
| + | * 0: the header was successfully read and printed. |
| + | * non-0: the header was not successfully read or was not printed. (Returns the SamStatus.) |
| + | |
| + | |
| + | === Example Output === |
| + | <pre> |
| + | @SQ SN:1 LN:247249719 |
| + | @SQ SN:2 LN:242951149 |
| + | @SQ SN:3 LN:199501827 |
| </pre> | | </pre> |
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