Changes

== Optional Region Specifying Parameters ==

== Optional Region Specifying Parameters ==

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=== Read only a Specific Reference/Chromosome (<code>--refName</code> or <code>--refID</code>) ===

=== Read only a Specific Reference/Chromosome (<code>--refName</code> or <code>--refID</code>) ===

If you only want to read a specific reference (chromosome), specify either <code>--refName</code> followed by the reference name or </code>--refID</code> followed by the reference id.

If you only want to read a specific reference (chromosome), specify either <code>--refName</code> followed by the reference name or </code>--refID</code> followed by the reference id.

Left shift indels as far as they can go in the read.  

Left shift indels as far as they can go in the read.  

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

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

Use <code>--excludeFlags</code> followed by the flags (as one integer) to skip any records that has any of the specified flags set.

Use <code>--excludeFlags</code> followed by the flags (as one integer) to skip any records that has any of the specified flags set.

=== Only Process Records with the all of the Specified Flags (<code>--requiredFlags</code>) ===

=== Only Process Records with the all of the Specified Flags (<code>--requiredFlags</code>) ===

Use <code>--requiredFlags</code> followed by the flags (as one integer) to only process records with all of the specified flags set.

Use <code>--requiredFlags</code> followed by the flags (as one integer) to only process records with all of the specified flags set.

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