gatk-3.8

Author	SHA1	Message	Date
asivache	843d7e6c8f	Now you can specify '-' instead of input file name, and the script will read from stdin git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1422 348d0f76-0448-11de-a6fe-93d51630548a	2009-08-14 20:30:56 +00:00
depristo	1d84c9da96	sortByRef now supports x:y location syntax git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1186 348d0f76-0448-11de-a6fe-93d51630548a	2009-07-07 16:42:40 +00:00
asivache	3098ed091c	checking in new folder for perl scripts AND a simple script that takes an input text file and reference dictionary (.fai) and performs stable sort of the input lines according to the contig order specified by the dictionary. Position of the contig filed to sort on in the input lines is specified as --k POS option. Input lines may specify contigs that are not in the dictionary, in this case the additional contigs will be added at the end of the sorted output, after all known contigs. The sorting order between these additional contigs is simply the order in which they first appear in the input git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@831 348d0f76-0448-11de-a6fe-93d51630548a	2009-05-27 16:34:55 +00:00