Pair-HMM alignment algorithm description fix (#5528)

* Fixed Pair-HMM algorithm description and reference See discussion https://gatkforums.broadinstitute.org/gatk/discussion/23197/question-about-the-alignment-performed-in-the-haplotypecaller-pairhmm#latest
broadinstitute · Jan 16, 2019 · 9b3ee90 · 9b3ee90
1 parent 74999b7
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Showing 3 changed files with 3 additions and 3 deletions.
diff --git a/src/main/java/org/broadinstitute/hellbender/utils/pairhmm/Log10PairHMM.java b/src/main/java/org/broadinstitute/hellbender/utils/pairhmm/Log10PairHMM.java
@@ -8,7 +8,7 @@
 import static org.broadinstitute.hellbender.utils.pairhmm.PairHMMModel.*;
 
 /**
- * Util class for performing the pair HMM for local alignment. Figure 4.3 in Durbin 1998 book.
+ * Util class for performing the pair HMM for global alignment. Figure 4.1 in Durbin 1998 book.
  */
 public final class Log10PairHMM extends N2MemoryPairHMM {
     /**

diff --git a/src/main/java/org/broadinstitute/hellbender/utils/pairhmm/PairHMM.java b/src/main/java/org/broadinstitute/hellbender/utils/pairhmm/PairHMM.java
@@ -20,7 +20,7 @@
 import java.util.function.Function;
 
 /**
- * Class for performing the pair HMM for local alignment. Figure 4.3 in Durbin 1998 book.
+ * Class for performing the pair HMM for global alignment. Figure 4.1 in Durbin 1998 book.
  */
 public abstract class PairHMM implements Closeable{
     protected static final Logger logger = LogManager.getLogger(PairHMM.class);

diff --git a/src/main/java/org/broadinstitute/hellbender/utils/pairhmm/VectorLoglessPairHMM.java b/src/main/java/org/broadinstitute/hellbender/utils/pairhmm/VectorLoglessPairHMM.java
@@ -20,7 +20,7 @@
 import java.util.Map;
 
 /**
- * Class for performing the pair HMM for local alignment using AVX instructions contained in a native shared library.
+ * Class for performing the pair HMM for global alignment using AVX instructions contained in a native shared library.
  */
 public final class VectorLoglessPairHMM extends LoglessPairHMM {