From f204908a9449d727691920de83a1dfdb1d1fed04 Mon Sep 17 00:00:00 2001
From: Mark DePristo <depristo@broadinstitute.org>
Date: Fri, 11 Jan 2013 14:19:32 -0500
Subject: [PATCH] Add some todos for future optimization to LIBS

---
 .../sting/utils/locusiterator/ReadStateManager.java | 13 +++++++++++++
 1 file changed, 13 insertions(+)

diff --git a/public/java/src/org/broadinstitute/sting/utils/locusiterator/ReadStateManager.java b/public/java/src/org/broadinstitute/sting/utils/locusiterator/ReadStateManager.java
index 74caef6a7..2dcf01d72 100644
--- a/public/java/src/org/broadinstitute/sting/utils/locusiterator/ReadStateManager.java
+++ b/public/java/src/org/broadinstitute/sting/utils/locusiterator/ReadStateManager.java
@@ -84,6 +84,7 @@ class ReadStateManager {
      * @return Iterator over the reads associated with that sample.
      */
     public Iterator<AlignmentStateMachine> iterator(final String sample) {
+        // TODO -- why is this wrapped?
         return new Iterator<AlignmentStateMachine>() {
             private Iterator<AlignmentStateMachine> wrappedIterator = readStatesBySample.get(sample).iterator();
 
@@ -138,6 +139,18 @@ class ReadStateManager {
     }
 
     // fast testing of position
+
+    /**
+     * TODO -- this function needs to be optimized
+     *
+     * Notes:
+     * -- the only place where it's called is in a block where we know isEmpty is false
+     * -- getFirst() is quite expensive, and it seems that we could cache this value in the outer
+     *    block, and then pass this in as an argument
+     *
+     * @param read
+     * @return
+     */
     private boolean readIsPastCurrentPosition(GATKSAMRecord read) {
         if (isEmpty())
             return false;