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== Read a SAM/BAM file and write as a SAM/BAM file ==
== convert ==
The <code>convert</code> option on the bam executable reads a SAM/BAM file and writes it as a SAM/BAM file.
./bam <bamFile>.bam <newSamFile>.sam
The executable converts the input file into the format of the output file. So if you want to convert a BAM file to a SAM file, from the pipeline/bam/ directory you just call:
./bam --in <bamFile>.bam --out <newSamFile>.sam
Don't forget to put in the paths to the executable and your test files.
Don't forget to put in the paths to the executable and your test files.
=== Parameters ===
<pre>
Required Parameters:
--in : the SAM/BAM file to be read
--out : the SAM/BAM file to be written
Optional Parameters:
--noeof : do not expect an EOF block on a bam file.
</pre>
=== Usage ===
=== Usage ===
./bam <inputFile> <outputFile.sam/bam/ubam (ubam is uncompressed bam)> [NOEOF]
./bam convert --in <inputFile> --out <outputFile.sam/bam/ubam (ubam is uncompressed bam)> [--noeof]
=== Return Value ===
=== Return Value ===
== Print SAM/BAM header==
== dumpHeader ==
The <code>dump_header</code> option on the bam executable prints the header of the specified SAM/BAM file to cout.
The <code>dumpHeader</code> option on the bam executable prints the header of the specified SAM/BAM file to cout.
=== Parameters ===
=== Parameters ===
== Split BAM by Chromosome ==
== splitChromosome ==
The <code>splitChromosome</code> option on the bam executable splits an indexed BAM file into multiple files based on the Chromosome (Reference Name).
The <code>splitChromosome</code> option on the bam executable splits an indexed BAM file into multiple files based on the Chromosome (Reference Name).
== Dump a BAM index file ==
== dumpIndex ==
The <code>dumpIndex</code> option on the bam executable prints BAM index file in an easy to read format.
=== Usage ===
=== Usage ===
./bam dump_index <bamIndexFile>
./bam dumpIndex <bamIndexFile>
=== Return Value ===
=== Return Value ===
== Read & Write indexed BAM file ==
== readIndexedBam ==
The <code>readIndexedBam</code> option on the bam executable reads an indexed BAM file reference id by reference id -1 to 22 and writes it out as a SAM/BAM file.
=== Usage ===
=== Usage ===
./bam read_indexed_bam <inputFilename> <outputFile.sam/bam> <bamIndexFile>
./bam readIndexedBam <inputFilename> <outputFile.sam/bam> <bamIndexFile>
=== Return Value ===
=== Return Value ===
* 0
* 0
