# HG changeset patch
# User Rayan Chikhi <chikhi@psu.edu>
# Date 1405970716 14400
# Node ID 6a9f7fd3d6b68af916967e8449786d9f81c1633e
# Parent  767bcb0a06df160ccd04552cf8843405f2d070f0# Parent  75aa585cfc169d3f951c91b3cef6406068966d70
merged

diff -r 75aa585cfc16 -r 6a9f7fd3d6b6 igvtools.jar
Binary file igvtools.jar has changed
diff -r 75aa585cfc16 -r 6a9f7fd3d6b6 picard_CollectAlignmentSummaryMetrics.xml
--- a/picard_CollectAlignmentSummaryMetrics.xml	Mon Jun 16 18:07:19 2014 -0400
+++ b/picard_CollectAlignmentSummaryMetrics.xml	Mon Jul 21 15:25:16 2014 -0400
@@ -60,7 +60,7 @@
       <param name="maxinsert" value="100000" />
       <param name="refGenomeSource" value="history" />
       <param name="ownFile" value="picard_input_hg18.trimmed.fasta" />
-      <param name="input_file" value="picard_input_tiny.sam" dbkey="hg18" />
+      <param name="input_file" value="picard_input_tiny.sam" dbkey="hg18" ftype="sam" />
       <output name="html_file" file="picard_output_alignment_summary_metrics.html" ftype="html" lines_diff="55"/>
     </test>
     <test>
@@ -71,7 +71,7 @@
       <param name="maxinsert" value="100000" />
       <param name="refGenomeSource" value="indexed" />
       <param name="index" value="hg19" />
-      <param name="input_file" value="picard_input_sorted_pair.sam" dbkey="hg19" />
+      <param name="input_file" value="picard_input_sorted_pair.sam" dbkey="hg19" ftype="sam" />
       <output name="html_file" file="picard_output_AsMetrics_indexed_hg18_sorted_pair.html" ftype="html" lines_diff="50"/>
     </test>
   </tests>
diff -r 75aa585cfc16 -r 6a9f7fd3d6b6 picard_wrapper.py
--- a/picard_wrapper.py	Mon Jun 16 18:07:19 2014 -0400
+++ b/picard_wrapper.py	Mon Jul 21 15:25:16 2014 -0400
@@ -804,7 +804,7 @@
     elif pic.picname == "DownsampleSam":
         cl.append('I=%s' % opts.input)
         output_string = opts.output
-        if opts.datatype == 'sam':
+        if opts.output_format == 'sam':
             output_string = output_string + ".sam"
         cl.append('O=%s' % output_string)
         if float(opts.probability) > 0:
@@ -812,9 +812,8 @@
         if float(opts.seed) > 0:
             cl.append('RANDOM_SEED=%s' % opts.seed)
         stdouts,rval = pic.runPic(opts.jar, cl)
-        if opts.input.endswith(".sam"):
-            renamed_output = output_string.replace(".sam", "")
-            os.rename(output_string,renamed_output)
+        if opts.output_format == 'sam':
+            os.rename(output_string, opts.output)
 
     elif pic.picname == 'MeanQualityByCycle':
         isPDF = 'MeanQualityByCycle.pdf'