Changes

The bam executable has the following functions.

The bam executable has the following functions.

* [[C++ Executable: bam#Read and Validate a SAM/BAM file|Read and Validate a SAM/BAM file]]

* [[C++ Executable: bam#validate|validate - 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#convert|convert - Read a SAM/BAM file and write as a SAM/BAM file]]

* [[C++ Executable: bam#Print SAM/BAM header|Print SAM/BAM header]]

* [[C++ Executable: bam#dumpHeader|dumpHeader - Print SAM/BAM header]]

* [[C++ Executable: bam#Split BAM by Chromosome|Split BAM by Chromosome]]

* [[C++ Executable: bam#splitChromosome|splitChromosome - Split BAM by Chromosome]]

* [[C++ Executable: bam#Write the alignments in the indexed BAM file that fall into the specified region|Write the alignments in the indexed BAM file that fall into the specified region]]

* [[C++ Executable: bam#writeRegion|writeRegion - Write the alignments in the indexed BAM file that fall into the specified region]]

* [[C++ Executable: bam#Dump a BAM index file|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#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#readIndexedBam|readIndexedBam - Read an indexed BAM file reference by reference id -1 to 22 and write it out as a SAM/BAM file]]

This executable is built using the [[C++ Library: bam|bam library]].

This executable is built using the [[C++ Library: bam|bam library]].