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The files all have the same base name, but with the chromosome name ".bam" or ".sam" appended.
The files all have the same base name, but with the chromosome name ".bam" or ".sam" appended.
= Usage =
./bam splitChromosome --in <inputFilename> --out <outputFileBaseName> [--noeof] [--bamout|--samout] [--params]
= Parameters =
= Parameters =
--params : print the parameter settings
--params : print the parameter settings
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{{PhoneHomeParamDesc}}
{{InBAMInputFile}}
== Output File Basename (<code>--out</code>) ==
Use <code>--out</code> followed by the base output filename (no extension) to specify the SAM/BAM basename to use for the output files.
= Usage =
The chromosome name and the appropriate extension (sam/bam) will be appended to the specified basename.
{{noeofBGZFParameter}}
== Output a BAM File (<code>--bamout</code>) ==
<code>--bamout</code> indicates to output a BAM file. This flag is enabled by default.
== Output a SAM File (<code>--samout</code>) ==
Use <code>--samout</code> to output a SAM file.
{{paramsParameter}}
{{PhoneHomeParameters}}
= Return Value =
= Return Value =
