aaron a0a549557f added a check of the sort ordering to the query methods, so that we detect if a file is unsorted much earlier. Also added some verbosity to the exception; it now contains an information about the raw attribute we saw for 'SO', the sort order of the bam file. ... Also fixed a bunch of documentation git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1015 348d0f76-0448-11de-a6fe-93d51630548a		2009-06-15 22:15:03 +00:00
..
config	Provide a default logger, some config settings, and some doc updates.	2009-04-29 02:06:05 +00:00
src/org/broadinstitute/sting	added a check of the sort ordering to the query methods, so that we detect if a file is unsorted much earlier. Also added some verbosity to the exception; it now contains an information about the raw attribute we saw for 'SO', the sort order of the bam file.	2009-06-15 22:15:03 +00:00
test/org/broadinstitute/sting	First pass of a walker for Eric that searches through an input BAM file for unclean reads, injecting the cleaned reads in their place and outputting the composite result.	2009-06-11 20:18:13 +00:00