Changes

=== Parameters ===

=== Parameters ===

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<pre>

Required Parameters:

    Required Parameters:

--refFile : the path/name of the reference file

        --refFile : the reference

        --refName  : the BAM reference Name to read (either this or refID can be specified)

--refID    : the reference ID to read, defaults to print all

        --start    : inclusive 0-based start position (defaults to -1)

--summary : only print a summary - 1 line per reference.

        --end      : exclusive 0-based end position (defaults to -1: meaning til the end of the reference)

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</pre>

=== Usage ===

=== Usage ===

  ./bam readReference --refFile <referenceFilename> --start <0 based start> --end <0 based end>|--numBases <number of bases>

  ./bam readReference --refFile <referenceFilename> --refName <reference Name>--start <0 based start> --end <0 based end>|--numBases <number of bases>

=== Return Value ===

=== Return Value ===

*    0: the reference file was successfully read.

*    0: the reference file was successfully read.

* non-0: the reference file was not successfully read.

* non-0: the reference file was not successfully read.