From ce160931d5c65cba4e355129b7328c2b56f08ead Mon Sep 17 00:00:00 2001
From: Mark DePristo <depristo@broadinstitute.org>
Date: Fri, 18 Jan 2013 16:52:49 -0500
Subject: [PATCH] Optimize creation of reads in ArtificialBAMBuilder

-- Now caches the reads so subsequent calls to makeReads() don't reallocate the reads from scratch each time
---
 .../sting/utils/sam/ArtificialBAMBuilder.java | 52 ++++++++++++-------
 1 file changed, 32 insertions(+), 20 deletions(-)

diff --git a/public/java/src/org/broadinstitute/sting/utils/sam/ArtificialBAMBuilder.java b/public/java/src/org/broadinstitute/sting/utils/sam/ArtificialBAMBuilder.java
index 82b5b29cc..bf3045c71 100644
--- a/public/java/src/org/broadinstitute/sting/utils/sam/ArtificialBAMBuilder.java
+++ b/public/java/src/org/broadinstitute/sting/utils/sam/ArtificialBAMBuilder.java
@@ -62,6 +62,7 @@ public class ArtificialBAMBuilder {
     int alignmentStart = 1;
     int readLength = 10;
     private final ArrayList<String> samples = new ArrayList<String>();
+    private List<GATKSAMRecord> createdReads = null;
 
     private LinkedList<GATKSAMRecord> additionalReads = new LinkedList<GATKSAMRecord>();
 
@@ -102,6 +103,7 @@ public class ArtificialBAMBuilder {
     }
 
     public ArtificialBAMBuilder createAndSetHeader(final int nSamples) {
+        createdReads = null;
         this.header = new SAMFileHeader();
         header.setSortOrder(SAMFileHeader.SortOrder.coordinate);
         header.setSequenceDictionary(parser.getContigs());
@@ -120,10 +122,12 @@ public class ArtificialBAMBuilder {
     }
 
     public void addReads(final GATKSAMRecord readToAdd) {
+        createdReads = null;
         additionalReads.add(readToAdd);
     }
 
     public void addReads(final Collection<GATKSAMRecord> readsToAdd) {
+        createdReads = null;
         additionalReads.addAll(readsToAdd);
     }
 
@@ -140,26 +144,34 @@ public class ArtificialBAMBuilder {
      * @return a ordered list of reads
      */
     public List<GATKSAMRecord> makeReads() {
-        final String baseName = "read";
-        List<GATKSAMRecord> reads = new ArrayList<GATKSAMRecord>(nReadsPerLocus*nLoci);
-        for ( int locusI = 0; locusI < nLoci; locusI++) {
-            final int locus = locusI * (skipNLoci + 1);
-            for ( int readI = 0; readI < nReadsPerLocus; readI++ ) {
-                for ( final SAMReadGroupRecord rg : header.getReadGroups() ) {
-                    final String readName = String.format("%s.%d.%d.%s", baseName, locus, readI, rg.getId());
-                    final GATKSAMRecord read = ArtificialSAMUtils.createArtificialRead(header, readName, 0, alignmentStart + locus, readLength);
-                    read.setReadGroup(new GATKSAMReadGroupRecord(rg));
-                    reads.add(read);
+        if ( createdReads == null ) {
+            final String baseName = "read";
+            final LinkedList<GATKSAMReadGroupRecord> readGroups = new LinkedList<GATKSAMReadGroupRecord>();
+            for ( final SAMReadGroupRecord rg : header.getReadGroups())
+                readGroups.add(new GATKSAMReadGroupRecord(rg));
+
+            List<GATKSAMRecord> reads = new ArrayList<GATKSAMRecord>(nReadsPerLocus*nLoci);
+            for ( int locusI = 0; locusI < nLoci; locusI++) {
+                final int locus = locusI * (skipNLoci + 1);
+                for ( int readI = 0; readI < nReadsPerLocus; readI++ ) {
+                    for ( final GATKSAMReadGroupRecord rg : readGroups ) {
+                        final String readName = String.format("%s.%d.%d.%s", baseName, locus, readI, rg.getId());
+                        final GATKSAMRecord read = ArtificialSAMUtils.createArtificialRead(header, readName, 0, alignmentStart + locus, readLength);
+                        read.setReadGroup(rg);
+                        reads.add(read);
+                    }
                 }
             }
+
+            if ( ! additionalReads.isEmpty() ) {
+                reads.addAll(additionalReads);
+                Collections.sort(reads, new SAMRecordCoordinateComparator());
+            }
+
+            createdReads = new ArrayList<GATKSAMRecord>(reads);
         }
 
-        if ( ! additionalReads.isEmpty() ) {
-            reads.addAll(additionalReads);
-            Collections.sort(reads, new SAMRecordCoordinateComparator());
-        }
-
-        return reads;
+        return createdReads;
     }
 
     /**
@@ -192,13 +204,13 @@ public class ArtificialBAMBuilder {
     public int getnReadsPerLocus() { return nReadsPerLocus; }
     public int getnLoci() { return nLoci; }
     public int getSkipNLoci() { return skipNLoci; }
-    public ArtificialBAMBuilder setSkipNLoci(int skipNLoci) { this.skipNLoci = skipNLoci; return this; }
+    public ArtificialBAMBuilder setSkipNLoci(int skipNLoci) { this.skipNLoci = skipNLoci; createdReads = null; return this; }
     public int getAlignmentStart() { return alignmentStart; }
-    public ArtificialBAMBuilder setAlignmentStart(int alignmentStart) { this.alignmentStart = alignmentStart; return this; }
+    public ArtificialBAMBuilder setAlignmentStart(int alignmentStart) { this.alignmentStart = alignmentStart; createdReads = null; return this; }
     public int getReadLength() { return readLength; }
-    public ArtificialBAMBuilder setReadLength(int readLength) { this.readLength = readLength; return this; }
+    public ArtificialBAMBuilder setReadLength(int readLength) { this.readLength = readLength; createdReads = null; return this; }
     public SAMFileHeader getHeader() { return header; }
-    public ArtificialBAMBuilder setHeader(SAMFileHeader header) { this.header = header; return this; }
+    public ArtificialBAMBuilder setHeader(SAMFileHeader header) { this.header = header; createdReads = null; return this; }
 
     public int getAlignmentEnd() {
         return alignmentStart + nLoci * (skipNLoci + 1) + readLength;