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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]]
* 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.
=== 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 ===
=== Example Output ===
