Changes

                  and exit when trying to run on an already mark-duplicated BAM

                  and exit when trying to run on an already mark-duplicated BAM

--excludeFlags <flag>    : exclude reads with any of these flags set when determining or marking duplicates

--excludeFlags <flag>    : exclude reads with any of these flags set when determining or marking duplicates

                          by default (0x304): exclude unmapped, secondary reads, and QC failures

                          by default (0xB04): exclude unmapped, secondary reads, QC failures, and supplementary reads

--verbose      : Turn on verbose mode

--verbose      : Turn on verbose mode

--noeof        : Do not expect an EOF block on a bam file.

--noeof        : Do not expect an EOF block on a bam file.

=== Skip Records with any of the Specified Flags (<code>--excludeFlags</code>)===

=== Skip Records with any of the Specified Flags (<code>--excludeFlags</code>)===

Skip records with any of the specified flags set, default 0x304

Skip records with any of the specified flags set, default 0xB04

By default skips reads with any of the following flags set:

By default skips reads with any of the following flags set:

* secondary alignment

* secondary alignment

* fails QC checks

* fails QC checks

This parameter was added in version 1.0.10.

This parameter was added in version 1.0.10.