Convert to htsjdk for BAM processing. Pilon release 1.12.

broadinstitute · Mar 29, 2015 · 46e5761 · 46e5761
1 parent d922206
commit 46e5761
Show file tree

Hide file tree

Showing 13 changed files with 13 additions and 13 deletions.
diff --git a/build.sbt b/build.sbt
@@ -1,6 +1,6 @@
 name := "pilon"
 
-version := "1.11"
+version := "1.12"
 
 scalaVersion := "2.10.4"
 

diff --git a/lib/htsjdk-1.130.jar b/lib/htsjdk-1.130.jar
diff --git a/lib/picard-1.98.jar b/lib/picard-1.98.jar
diff --git a/lib/sam-1.98.jar b/lib/sam-1.98.jar
diff --git a/src/main/scala/org/broadinstitute/pilon/Assembler.scala b/src/main/scala/org/broadinstitute/pilon/Assembler.scala
@@ -20,7 +20,7 @@ package org.broadinstitute.pilon
 import scala.annotation.tailrec
 import collection.JavaConversions._
 import collection.mutable.{ Map, HashMap, Set, HashSet }
-import net.sf.samtools._
+import htsjdk.samtools._
 
 object Assembler {
   var K = 47

diff --git a/src/main/scala/org/broadinstitute/pilon/BamFile.scala b/src/main/scala/org/broadinstitute/pilon/BamFile.scala
@@ -21,7 +21,7 @@ package org.broadinstitute.pilon
 import collection.mutable.Map
 import java.io.File
 import scala.collection.JavaConversions._
-import net.sf.samtools._
+import htsjdk.samtools._
 
 object BamFile {
   val indexSuffix = ".bai"
@@ -35,8 +35,8 @@ class BamFile(val bamFile: File, val bamType: Symbol) {
   var baseCount: Long = 0
 
   def reader = {
-    val r = new SAMFileReader(bamFile, new File(path + BamFile.indexSuffix))
-    r.setValidationStringency(SAMFileReader.ValidationStringency.SILENT)
+    //val r = new SAMFileReader(bamFile, new File(path + BamFile.indexSuffix))
+    val r = SamReaderFactory.makeDefault().validationStringency(ValidationStringency.SILENT).open(bamFile)
     r
   }
 

diff --git a/src/main/scala/org/broadinstitute/pilon/GapFiller.scala b/src/main/scala/org/broadinstitute/pilon/GapFiller.scala
@@ -20,7 +20,7 @@ package org.broadinstitute.pilon
 
 import collection.JavaConversions._
 import collection.mutable.Map
-import net.sf.samtools._
+import htsjdk.samtools._
 
 
 object GapFiller {

diff --git a/src/main/scala/org/broadinstitute/pilon/GenomeFile.scala b/src/main/scala/org/broadinstitute/pilon/GenomeFile.scala
@@ -23,7 +23,7 @@ import java.io.{File,PrintWriter,FileWriter,BufferedWriter}
 import scala.collection.JavaConversions._
 import scala.collection.mutable.Map
 import scala.util.Random
-import net.sf.picard.reference._
+import htsjdk.samtools.reference._
 import Utils._
 
 class GenomeFile(val referenceFile: File, val targets : String = "") {

diff --git a/src/main/scala/org/broadinstitute/pilon/GenomeRegion.scala b/src/main/scala/org/broadinstitute/pilon/GenomeRegion.scala
@@ -19,7 +19,7 @@
 package org.broadinstitute.pilon
 
 import collection.mutable.Map
-import net.sf.picard.reference._
+import htsjdk.samtools.reference._
 import Utils._
 import java.io.PrintWriter
 

diff --git a/src/main/scala/org/broadinstitute/pilon/PileUpRegion.scala b/src/main/scala/org/broadinstitute/pilon/PileUpRegion.scala
@@ -19,7 +19,7 @@
 package org.broadinstitute.pilon
 
 import scala.collection.JavaConversions._
-import net.sf.samtools._
+import htsjdk.samtools._
 import Utils._
 
 class PileUpRegion(name: String, start: Int, stop: Int)
@@ -45,7 +45,7 @@ class PileUpRegion(name: String, start: Int, stop: Int)
       }
     }
   }
-
+  
   def remove(locus: Int, base: Char, qual: Int, mq: Int,
     pair: Boolean) = {
     if (inRegion(locus)) {

diff --git a/src/main/scala/org/broadinstitute/pilon/Pilon.scala b/src/main/scala/org/broadinstitute/pilon/Pilon.scala
@@ -54,7 +54,7 @@ object Pilon {
   var strays = true
   var threads = 1
   var trSafe = true
-  
+
   // Global computed data
   var novelContigs = List[String]()
 

diff --git a/src/main/scala/org/broadinstitute/pilon/Scaffold.scala b/src/main/scala/org/broadinstitute/pilon/Scaffold.scala
@@ -29,7 +29,7 @@ package org.broadinstitute.pilon
 
 import scala.collection.JavaConversions._
 import collection.mutable.{ Map, HashMap, Set, HashSet }
-import net.sf.samtools._
+import htsjdk.samtools._
 
 
 class MatePair(r1: SAMRecord, r2: SAMRecord) {

diff --git a/src/main/scala/org/broadinstitute/pilon/Tracks.scala b/src/main/scala/org/broadinstitute/pilon/Tracks.scala
@@ -28,7 +28,7 @@ package org.broadinstitute.pilon
 import java.io._
 
 import scala.collection.JavaConversions._
-import net.sf.samtools._
+import htsjdk.samtools._
 
 class Tracks(val reference: GenomeFile, val prefix : String = "") {
   def standardTracks = {