7cab994d88
Add argument to sortByRef for specifying the tmp directory for sorting.
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Update the liftover script to reflect this addition.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3323 348d0f76-0448-11de-a6fe-93d51630548a
2010-05-07 13:53:26 +00:00
843d7e6c8f
Now you can specify '-' instead of input file name, and the script will read from stdin
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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
1d84c9da96
sortByRef now supports x:y location syntax
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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
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
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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
ebanks
asivache
depristo