Added support for fasta reading for TCS creation in the main script.

Author: StuntsPT

4Pipe4.py

@@ -233,7 +233,9 @@ def DiscoveryTCS(basefile):
     print("\nRunning SNP Discovery tool module...")
     SAM_to_BAM.RunModule(basefile + '.sam',
                          basefile + '.bam')
-    BAM_to_TCS.RunModule(basefile + '.bam')
+    BAM_to_TCS.RunModule(basefile + '.bam', basefile + '_assembly/' +
+                         miraproject + '_d_results/' + miraproject +
+                         '_out.padded.fasta')
     TCS.RunModule(basefile + '.tcs', basefile + '_out.short.tcs',
                   int(config.get('Variables', 'minqual')),
                   int(config.get('Variables', 'mincov')))