Changes

:Further Explanation of the issue<nowiki>:</nowiki>

:Further Explanation of the issue<nowiki>:</nowiki>

::The SAMTOOLS_VIEW_TARGET_ONLY set to TRUE tells our pipeline to pass to SAMTOOLS view all of the regions in the BED file that fall into a single segment of our processing.   

::The SAMTOOLS_VIEW_TARGET_ONLY set to TRUE tells our pipeline to pass to SAMTOOLS view all of the regions in the BED file that fall into a single segment of our processing.   

::It appears that samtools view will then go through each of those regions independently and one a ta time, selecting just the records that fall within that region.   

::It appears that samtools view will then go through each of those regions independently and one at a time, selecting just the records that fall within that region.   

::A problem occurs if records fall within multiple regions from the BED file.  Since samtools view process the regions independently, it will write those records multiple times and they will end up out of order.

::A problem occurs if records fall within multiple regions from the BED file.  Since samtools view process the regions independently, it will write those records multiple times and they will end up out of order.