Version 1.18.

broadinstitute · Jun 12, 2016 · bdac949 · bdac949
1 parent f93fe2f
commit bdac949
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Showing 3 changed files with 13 additions and 6 deletions.
diff --git a/build.sbt b/build.sbt
@@ -1,6 +1,6 @@
 name := "pilon"
 
-version := "1.17"
+version := "1.18"
 
 scalaVersion := "2.11.8"
 

diff --git a/src/main/scala/org/broadinstitute/pilon/GenomeFile.scala b/src/main/scala/org/broadinstitute/pilon/GenomeFile.scala
@@ -113,9 +113,9 @@ class GenomeFile(val referenceFile: File, val targets : String = "") {
       bamFiles foreach { r.processBam(_) }
       r.postProcess
       if (Pilon.vcf || !Pilon.fixList.isEmpty) {
-    	r.identifyAndFixIssues
-    	// If we don't need pileups for VCF later, free up the memory now!
-    	if (!Pilon.vcf) r.finalizePileUps
+        r.identifyAndFixIssues
+        // If we don't need pileups for VCF later, free up the memory now!
+        if (!Pilon.vcf) r.finalizePileUps
       }
       println(r + " log:")
       r.printLog

diff --git a/src/main/scala/org/broadinstitute/pilon/GenomeRegion.scala b/src/main/scala/org/broadinstitute/pilon/GenomeRegion.scala
@@ -311,8 +311,15 @@ class GenomeRegion(val contig: ReferenceSequence, start: Int, stop: Int)
           if (fix) snpFixList ::= (locus(i), rBase.toString, cBase.toString)
           snps += 1
         case 'amb =>
-          val calledBase = if (Pilon.iupac) Bases.toIUPAC(cBase, bc.altBase) else cBase
-          if (fix) snpFixList ::= (locus(i), rBase.toString, calledBase.toString)
+          if (fix) {
+            if (Pilon.iupac) {
+              // we put these on the small fix list because iupac codes can mess up assembly
+              // flank anchor kmers
+              smallFixList ::= (locus(i), rBase.toString, Bases.toIUPAC(cBase, bc.altBase).toString)
+            } else {
+              snpFixList ::= (locus(i), rBase.toString, cBase.toString)
+            }
+          }
           amb += 1
         case 'ins =>
           val insert = bc.insertion