From 897ef07183049223af88426cd462700851603fa1 Mon Sep 17 00:00:00 2001
From: Steve Huang <shuang@broadinstitute.org>
Date: Tue, 5 Sep 2017 17:57:16 -0400
Subject: [PATCH] ready to go

---
 .../SimpleStrandSwitchVariantDetector.java    | 23 ++++++++++++-------
 1 file changed, 15 insertions(+), 8 deletions(-)

diff --git a/src/main/java/org/broadinstitute/hellbender/tools/spark/sv/discovery/prototype/SimpleStrandSwitchVariantDetector.java b/src/main/java/org/broadinstitute/hellbender/tools/spark/sv/discovery/prototype/SimpleStrandSwitchVariantDetector.java
index 8a6bf7ad7ef..7563e1f542c 100644
--- a/src/main/java/org/broadinstitute/hellbender/tools/spark/sv/discovery/prototype/SimpleStrandSwitchVariantDetector.java
+++ b/src/main/java/org/broadinstitute/hellbender/tools/spark/sv/discovery/prototype/SimpleStrandSwitchVariantDetector.java
@@ -76,7 +76,6 @@ public boolean test(final AlignedContig contig) {
     /**
      * Removes overlap from a designated alignment interval, so that the inverted duplicated reference span is minimal.
      * If the two alignment intervals are NOT overlapping, return the original aligned contig.
-     * For algorithm {@see <a href="https://github.com/broadinstitute/dsde-methods-sv/pull/8"}
      */
     private static AlignedContig removeOverlap(final AlignedContig contig) {
         final int overlapOnRead = AlignmentInterval.overlapOnContig(contig.alignmentIntervals.get(0),
@@ -86,12 +85,12 @@ private static AlignedContig removeOverlap(final AlignedContig contig) {
         } else {
             final AlignmentInterval one = contig.alignmentIntervals.get(0),
                                     two = contig.alignmentIntervals.get(1);
-            // js is for "the shoot-off reference location of a jump that linked to alignment intervals", and
-            // jl is for "that jump's landing reference location"
-            final int js = one.referenceSpan.getEnd(),
-                      jl = two.referenceSpan.getStart();
+            // jumpStart is for "the starting reference location of a jump that linked two alignment intervals", and
+            // jumpLandingRefLoc is for "that jump's landing reference location"
+            final int jumpStartRefLoc   = one.referenceSpan.getEnd(),
+                      jumpLandingRefLoc = two.referenceSpan.getStart();
             final AlignmentInterval reconstructedOne, reconstructedTwo;
-            if (js <= jl ^ one.forwardStrand) {
+            if (jumpStartRefLoc <= jumpLandingRefLoc ^ one.forwardStrand) {
                 reconstructedOne = one;
                 reconstructedTwo = clipAlignmentInterval(two, overlapOnRead, false);
             } else {
@@ -167,8 +166,16 @@ static Tuple2<SimpleInterval, Cigar> computeNewRefSpanAndCigar(final AlignmentIn
 
                     // deal with cigar first
                     newMiddleSection.add( new CigarElement(clipLengthOnRead, CigarOperator.S) );
-                    final int a = readBasesConsumed + ce.getLength() - clipLengthOnRead;
-                    if (a!=0) newMiddleSection.add( new CigarElement(a, ce.getOperator().isAlignment() ? CigarOperator.M : CigarOperator.S) );
+                    // # of bases left, for the current operation, after requested clipping is done,
+                    // may be 0 because we probably don't need the entire current operation to have the requested
+                    // number of read bases clipped, e.g. we only 15 more bases from the current operation,
+                    // but its length is 20, then 5 bases should be "left over"
+                    final int leftOverBasesForCurrOp = readBasesConsumed + ce.getLength() - clipLengthOnRead;
+                    if (leftOverBasesForCurrOp!=0) {
+                        newMiddleSection.add(// again note that here we can have only either 'M' or 'I'
+                                new CigarElement(leftOverBasesForCurrOp, ce.getOperator().isAlignment() ? CigarOperator.M
+                                                                                                        : CigarOperator.S) );
+                    }
                     newMiddleSection.addAll( cigarElements.subList(idx+1, cigarElements.size()) );
 
                     // then deal with ref span