Changes

* Rewrite SAM/BAM Files

* Rewrite SAM/BAM Files

** [[BamUtil: convert|convert - Read a SAM/BAM file and write as a SAM/BAM file (optionally converts between '=' & bases in the sequence)]]

** [[BamUtil: convert|'''convert''' - Read a SAM/BAM file and write as a SAM/BAM file (optionally converts between '=' & bases in the sequence)]]

** [[BamUtil: splitChromosome|splitChromosome - Split BAM by Chromosome]]

** [[BamUtil: splitChromosome|'''splitChromosome''' - Split BAM by Chromosome]]

** [[BamUtil: writeRegion|writeRegion - Write the alignments in the indexed BAM file that fall into the specified region and/or have the specified read name]]

** [[BamUtil: writeRegion|'''writeRegion''' - Write the alignments in the indexed BAM file that fall into the specified region and/or have the specified read name]]

** [[BamUtil: filter|filter - Filter reads by clipping ends with too high of a mismatch percentage and by marking reads unmapped if the quality of mismatches is too high]]

** [[BamUtil: filter|'''filter''' - Filter reads by clipping ends with too high of a mismatch percentage and by marking reads unmapped if the quality of mismatches is too high]]

** [[BamUtil: revert|revert - Revert SAM/BAM replacing the specified fields with their previous values (if known) and removes specified tags]]

** [[BamUtil: revert|'''revert''' - Revert SAM/BAM replacing the specified fields with their previous values (if known) and removes specified tags]]

** [[BamUtil: squeeze|squeeze -  reduces files size by dropping OQ fields, duplicates, specified tags, using '=' when a base matches the reference, binning quality scores, and replacing readNames with unique integers]]

** [[BamUtil: squeeze|'''squeeze''' -  reduces files size by dropping OQ fields, duplicates, specified tags, using '=' when a base matches the reference, binning quality scores, and replacing readNames with unique integers]]

** [[BamUtil: findCigars|findCigars - Output just the reads that contain any of the specified CIGAR operations]]

** [[BamUtil: findCigars|'''findCigars''' - Output just the reads that contain any of the specified CIGAR operations]]

** [[BamUtil: readIndexedBam|readIndexedBam - Read an indexed BAM file reference by reference id -1 to the max reference id and write it out as a SAM/BAM file]]

** [[BamUtil: readIndexedBam|'''readIndexedBam''' - Read an indexed BAM file reference by reference id -1 to the max reference id and write it out as a SAM/BAM file]]

* Informational Tools

* Informational Tools

** [[BamUtil: validate|validate|validate - Read and Validate a SAM/BAM file]]

** [[BamUtil: validate|'''validate''' - Read and Validate a SAM/BAM file]]

** [[BamUtil: diff|diff - Print the diffs between 2 bams]]

** [[BamUtil: diff|'''diff''' - Print the diffs between 2 bams]]

** [[BamUtil: stats|stats - Print the diffs between 2 bams]]

** [[BamUtil: stats|'''stats''' - Print the diffs between 2 bams]]

* Print Information in Readable Form:

* Print Information in Readable Form:

** [[BamUtil: dumpHeader|dumpHeader - Print SAM/BAM header]]

** [[BamUtil: dumpHeader|'''dumpHeader''' - Print SAM/BAM header]]

** [[BamUtil: dumpRefInfo|dumpRefInfo - Print SAM/BAM Reference Information]]

** [[BamUtil: dumpRefInfo|'''dumpRefInfo''' - Print SAM/BAM Reference Information]]

** [[BamUtil: dumpIndex|dumpIndex - Dump a BAM index file into an easy to read text version]]

** [[BamUtil: dumpIndex|'''dumpIndex''' - Dump a BAM index file into an easy to read text version]]

** [[BamUtil: readReference|readReference - Print the reference string for the specified region]]

** [[BamUtil: readReference|'''readReference''' - Print the reference string for the specified region]]