From ee6a90a8144fd26a5b80b69b5ba0d3a53d3e8b78 Mon Sep 17 00:00:00 2001
From: Nils Homer <nilshomer@gmail.com>
Date: Thu, 18 May 2017 12:37:07 -0700
Subject: [PATCH] Add auxiliary baits and targets to BaitDesigner.

This is useful if you re-designing just a sub-set of your targets.
---
 src/main/java/picard/util/BaitDesigner.java | 44 ++++++++++++++++++++++++++++-
 1 file changed, 43 insertions(+), 1 deletion(-)

diff --git a/src/main/java/picard/util/BaitDesigner.java b/src/main/java/picard/util/BaitDesigner.java
index 2dbb05584..d096fae07 100644
--- a/src/main/java/picard/util/BaitDesigner.java
+++ b/src/main/java/picard/util/BaitDesigner.java
@@ -1,6 +1,8 @@
 package picard.util;
 
+import htsjdk.samtools.SAMFileHeader;
 import htsjdk.samtools.SAMSequenceDictionary;
+import htsjdk.samtools.SamFlagField;
 import htsjdk.samtools.reference.ReferenceSequence;
 import htsjdk.samtools.reference.ReferenceSequenceFileWalker;
 import htsjdk.samtools.util.CloserUtil;
@@ -274,6 +276,12 @@ public String toString() {
     @Option(shortName = "T", doc = "The file with design parameters and targets")
     public File TARGETS;
 
+    @Option(shortName = "AUX_T", doc = "The file with targets to include when calculating statistics (ex. re-design)", optional = true)
+    public File AUX_TARGETS;
+
+    @Option(shortName = "AUX_B", doc = "The file with baits to include when calculating statistics (ex. re-design)", optional = true)
+    public File AUX_BAITS;
+
     @Option(doc = "The name of the bait design")
     public String DESIGN_NAME;
 
@@ -428,7 +436,7 @@ protected int doWork() {
 
             if (MERGE_NEARBY_TARGETS) {
                 final ListIterator<Interval> iterator = padded.getIntervals().listIterator();
-                Interval previous = iterator.next();
+                Interval previous = iterator.hasNext() ? iterator.next() : null;
 
                 targets = new IntervalList(padded.getHeader());
 
@@ -489,6 +497,40 @@ protected int doWork() {
             }
         }
 
+        if (AUX_BAITS != null) {
+            final IntervalList auxBaits = IntervalList.fromFile(AUX_BAITS);
+            SequenceUtil.assertSequenceDictionariesEqual(auxBaits.getHeader().getSequenceDictionary(),
+                    baits.getHeader().getSequenceDictionary());
+
+            final ReferenceSequenceFileWalker walker = new ReferenceSequenceFileWalker(REFERENCE_SEQUENCE);
+            ReferenceSequence reference = null;
+            final SAMSequenceDictionary dict = auxBaits.getHeader().getSequenceDictionary();
+            for (final Interval interval : auxBaits.getIntervals()) {
+                final int contigIndex = dict.getSequenceIndex(interval.getContig());
+                if (reference == null || contigIndex != reference.getContigIndex()) {
+                    reference = walker.get(contigIndex);
+                }
+                final Bait bait = new Bait(interval.getContig(),
+                        interval.getStart(),
+                        interval.getEnd(),
+                        interval.isNegativeStrand(),
+                        interval.getName()
+                );
+                bait.addBases(reference, DESIGN_ON_TARGET_STRAND);
+                baits.add(bait);
+            }
+            log.info("Added " + auxBaits.size() + " auxiliary baits");
+        }
+
+        if (AUX_TARGETS != null) {
+            final IntervalList auxTargets = IntervalList.fromFile(AUX_TARGETS);
+            SequenceUtil.assertSequenceDictionariesEqual(auxTargets.getHeader().getSequenceDictionary(),
+                    targets.getHeader().getSequenceDictionary());
+            targets.addall(auxTargets.getIntervals());
+            log.info("Added " + auxTargets.size() + " auxiliary targets");
+
+        }
+
         calculateStatistics(targets, baits);
         log.info("Designed and kept " + baits.size() + " baits, discarded " + discardedBaits);