Changes

Clipping By Coordinate Optional Parameters:

Clipping By Coordinate Optional Parameters:

--poolSize    : Maximum number of records the program is allowed to allocate

--poolSize    : Maximum number of records the program is allowed to allocate

                for clipping on Coordinate sorted files. (Default: 5000)

                for clipping on Coordinate sorted files. (Default: 1000000)

--poolSkipClip : Skip clipping reads to free of usable records when the

--poolSkipClip : Skip clipping reads to free of usable records when the

                poolSize is hit. The default action is to just clip the

                poolSize is hit. The default action is to just clip the

== Set the SAM/BAMs record buffer size (<code>--poolSize</code>) ==

== Set the SAM/BAMs record buffer size (<code>--poolSize</code>) ==

To handle coordinate sorted files, SAM/BAM records are buffered until it is known that all following records will have a later start position.  To prevent the program from running away with memory, a limit is set to the number of records that can be buffered (defaults to 5000).

To handle coordinate sorted files, SAM/BAM records are buffered until it is known that all following records will have a later start position.  To prevent the program from running away with memory, a limit is set to the number of records that can be buffered (defaults to 1000000).

If the poolSize is exhausted, the code will write the earliest record awaiting its overlapping mate and any previous records that are being buffered.

If the poolSize is exhausted, the code will write the earliest record awaiting its overlapping mate and any previous records that are being buffered.