Difference between revisions of "BamUtil"

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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.
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* [[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.
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* [[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 ===
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== Read a SAM/BAM file and write as a SAM/BAM file ==
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=== Usage ===
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./bam <inputFile> <outputFile.sam/bam>
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=== Return Value ===
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=== Example Output ===
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== Dump a BAM index file ==
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=== Usage ===
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./bam dump_index <bamIndexFile>
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=== Return Value ===
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* -1 if the bam index file could not be opened.
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* 0 if the bam index file could be opened.
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=== Example Output ===
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== Read & Write indexed BAM file ==
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=== Usage ===
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./bam read_indexed_bam <inputFilename> <outputFile.sam/bam> <bamIndexFile>
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=== Return Value ===
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* 0
  
 
=== Example Output ===
 
=== Example Output ===

Revision as of 13:43, 6 April 2010

bam Executable

The bam executable has the following functions.


Read and Validate a SAM/BAM file

The validate option on the bam executable validates a SAM/BAM file.

The validation checks that the file is sorted as specified in the user options. Default is unsorted, in which case, no order validation is done.

NOTE: Currently the only validation that is done is that the file is sorted as specified in the user specified options.


Usage

./bam validate --in <inputFile> [--so_flag|--so_unsorted|--so_coord|--so_query]


Return Value

  • 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.


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

Example Output