Mercurial > repos > chrisw > monorail_test

diff monorail.sh @ 5:d2d9937d1f9c draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Uploaded
author chrisw
date Tue, 12 Feb 2019 13:51:52 -0500
parents ae546ad6f2f4
children
line wrap: on
line diff
--- a/monorail.sh	Tue Feb 12 11:56:25 2019 -0500
+++ b/monorail.sh	Tue Feb 12 13:51:52 2019 -0500
@@ -29,4 +29,4 @@
 samtools index -@ $threads $sorted_bam >> stools.log 2>&1
 
 #get coverage summaries
-bamcount $sorted_bam --threads $threads --coverage --no-head --require-mdz --min-unique-qual $min_uniq_qual --frag-dist bc --bigwig bc --annotation $annotation bc --auc bc --lats bc > bc.log 2>&1 
+bamcount $sorted_bam --threads $threads --coverage --no-head --require-mdz --min-unique-qual $min_uniq_qual --frag-dist bc --bigwig bc --annotation $annotation bc --auc bc --alts bc > bc.log 2>&1