Merge branch 'master' into rodrewrite

build.xml

@@ -163,6 +163,14 @@
       <!-- Remove old versions of ivy jars AFTER the ivy:retrieve has been class loaded. -->
       <delete file="${ivy.jar.dir}/ivy-2.0.0.jar"/>
       <delete file="${ivy.jar.dir}/ivy-2.2.0-rc1.jar"/>
+      <!--
+         An old versions of the ivy-1.4.1.xml does not contain /ivy-module/configuration/conf/@name="compile".
+         Easier to upgrade to 1.4.4 than try to deal with xmlproperty and conditional deletion in ant.
+         Just in case we remove explicit 1.4.4 and go back to 1.4.1, try to clean out the file for now.
+        -->
+      <delete file="${ivy.home}/cache/javax.mail/mail/ivy-1.4.1.xml"/>
+      <delete file="${ivy.home}/cache/javax.mail/mail/ivydata-1.4.1.properties"/>
+      <delete file="${ivy.home}/cache/javax.mail/mail/jars/mail-1.4.1.jar"/>
     </target>
 
     <target name="init.buildall">

ivy.xml

@@ -15,10 +15,8 @@
     <!-- Tribble -->
     <dependency org="org.broad" name="tribble" rev="latest.integration"/>
 
-    <dependency org="log4j" name="log4j" rev="1.2.15">
+    <dependency org="log4j" name="log4j" rev="1.2.15"/>
-      <!-- Don't include javax.mail here in default, only used in scala->default by commons-email -->
+    <dependency org="javax.mail" name="mail" rev="1.4.4"/>
-      <exclude org="javax.mail" />
-    </dependency>
     <dependency org="colt" name="colt" rev="1.2.0"/>
     <dependency org="jboss" name="javassist" rev="3.7.ga"/>
     <dependency org="org.simpleframework" name="simple-xml" rev="2.0.4"/>

public/java/src/org/broadinstitute/sting/utils/sam/ReadUtils.java

@@ -118,31 +118,40 @@ public class ReadUtils {
     /**
      * This enum represents all the different ways in which a read can overlap an interval.
      *
-     * NO_OVERLAP:
+     * NO_OVERLAP_CONTIG:
+     * read and interval are in different contigs.
+     *
+     * NO_OVERLAP_LEFT:
+     * the read does not overlap the interval.
+     *
+     *                        |----------------| (interval)
+     *   <---------------->                      (read)
+     *
+     * NO_OVERLAP_RIGHT:
      * the read does not overlap the interval.
      *
      *   |----------------|                      (interval)
      *                        <----------------> (read)
      *
-     * LEFT_OVERLAP:
+     * OVERLAP_LEFT:
      * the read starts before the beginning of the interval but ends inside of it
      *
      *          |----------------| (interval)
      *   <---------------->        (read)
      *
-     * RIGHT_OVERLAP:
+     * OVERLAP_RIGHT:
      * the read starts inside the interval but ends outside of it
      *
      *   |----------------|     (interval)
      *       <----------------> (read)
      *
-     * FULL_OVERLAP:
+     * OVERLAP_LEFT_AND_RIGHT:
      * the read starts before the interval and ends after the interval
      *
      *      |-----------|     (interval)
      *  <-------------------> (read)
      *
-     * CONTAINED:
+     * OVERLAP_CONTAINED:
      * the read starts and ends inside the interval
      *
      *  |----------------|     (interval)
@@ -658,7 +667,7 @@ public class ReadUtils {
             return ReadAndIntervalOverlap.OVERLAP_RIGHT;
     }
 
-    @Ensures({"result >= read.getUnclippedStart()", "result <= read.getUnclippedEnd()"})
+    @Ensures({"result >= read.getUnclippedStart()", "result <= read.getUnclippedEnd() || readIsEntirelyInsertion(read)"})
     public static int getRefCoordSoftUnclippedStart(SAMRecord read) {
         int start = read.getUnclippedStart();
         for (CigarElement cigarElement : read.getCigar().getCigarElements()) {
@@ -670,9 +679,13 @@ public class ReadUtils {
         return start;
     }
 
-    @Ensures({"result >= read.getUnclippedStart()", "result <= read.getUnclippedEnd()"})
+    @Ensures({"result >= read.getUnclippedStart()", "result <= read.getUnclippedEnd() || readIsEntirelyInsertion(read)"})
     public static int getRefCoordSoftUnclippedEnd(SAMRecord read) {
         int stop = read.getUnclippedStart();
+
+        if (readIsEntirelyInsertion(read))
+            return stop;
+
         int shift = 0;
         CigarOperator lastOperator = null;
         for (CigarElement cigarElement : read.getCigar().getCigarElements()) {
@@ -686,6 +699,14 @@ public class ReadUtils {
         return (lastOperator == CigarOperator.HARD_CLIP) ? stop-1 : stop+shift-1 ;
     }
 
+    private static boolean readIsEntirelyInsertion(SAMRecord read) {
+        for (CigarElement cigarElement : read.getCigar().getCigarElements()) {
+            if (cigarElement.getOperator() != CigarOperator.INSERTION)
+                return false;
+        }
+        return true;
+    }
+
     /**
      * Looks for a read coordinate that corresponds to the reference coordinate in the soft clipped region before
      * the alignment start of the read.

public/scala/qscript/org/broadinstitute/sting/queue/qscripts/GATKResourcesBundle.scala

@@ -131,11 +131,11 @@ class GATKResourcesBundle extends QScript {
     addResource(new Resource("/humgen/gsa-hpprojects/GATK/data/Comparisons/Validated/HapMap/3.3/genotypes_r27_nr.b37_fwd.vcf",
       "hapmap_3.3", b37, true, true))
 
-    addResource(new Resource("/humgen/gsa-hpprojects/GATK/data/Comparisons/Unvalidated/AFR+EUR+ASN+1KG.dindel_august_release_merged_pilot1.20110126.sites.vcf",
+    addResource(new Resource("/humgen/1kg/processing/official_release/phase1/ALL.wgs.VQSR_consensus_biallelic.20101123.indels.sites.vcf",
-      "1000G_indels_for_realignment", b37, true, false))
+      "1000G_biallelic.indels", b37, true, false))
 
     addResource(new Resource("/humgen/gsa-hpprojects/GATK/data/Comparisons/Validated/Mills_Devine_Indels_2011/ALL.wgs.indels_mills_devine_hg19_leftAligned_collapsed_double_hit.sites.vcf",
-      "indels_mills_devine", b37, true, true))
+      "Mills_Devine_2hit.indels", b37, true, true))
     
     //
     // example call set for wiki tutorial
@@ -300,9 +300,9 @@ class GATKResourcesBundle extends QScript {
     bamFile = bamIn
   }
 
-  class IndexVCF(@Input vcf: File, @Input ref: File) extends CountRod with UNIVERSAL_GATK_ARGS {
+  class IndexVCF(@Input vcf: File, @Input ref: File) extends CountRODs with UNIVERSAL_GATK_ARGS {
     //@Output val vcfIndex: File = swapExt(vcf.getParent, vcf, ".vcf", ".vcf.idx")
-    this.rodBind :+= RodBind(vcf.getName, "VCF", vcf)
+    this.rod :+= vcf
     this.reference_sequence = ref
   }
 
@@ -313,7 +313,7 @@ class GATKResourcesBundle extends QScript {
   }
 
   class MakeDBSNP129(@Input dbsnp: File, @Input ref: File, @Output dbsnp129: File) extends SelectVariants with UNIVERSAL_GATK_ARGS {
-    this.rodBind :+= RodBind("variant", "VCF", dbsnp)
+    this.variant = dbsnp
     this.select ++= List("\"dbSNPBuildID <= 129\"")
     this.reference_sequence = ref
     this.out = dbsnp129