From 03e9a326ec1922fa70da4f5573c0516066c034f2 Mon Sep 17 00:00:00 2001
From: Louis Bergelson <louisb@broadinstitute.org>
Date: Wed, 30 Oct 2019 16:57:10 -0400
Subject: [PATCH] Add back a method which was accidentally replaced (#1433)

* While adding Path variants of File methods in #1430 we accidentally replaced a method instead of adding a new one.
* Add that method back in and 1 additional overload which we missed.
---
 .../htsjdk/tribble/index/IndexFactory.java    | 29 +++++++++++++++++++
 1 file changed, 29 insertions(+)

diff --git a/src/main/java/htsjdk/tribble/index/IndexFactory.java b/src/main/java/htsjdk/tribble/index/IndexFactory.java
index 99ce636691..e48acc0a25 100644
--- a/src/main/java/htsjdk/tribble/index/IndexFactory.java
+++ b/src/main/java/htsjdk/tribble/index/IndexFactory.java
@@ -343,6 +343,7 @@ public static <FEATURE_TYPE extends Feature, SOURCE_TYPE> Index createDynamicInd
         return createDynamicIndex(inputPath, codec, IndexBalanceApproach.FOR_SEEK_TIME);
     }
 
+
     /**
      * Create a index of the specified type with default binning parameters
      *
@@ -356,6 +357,34 @@ public static <FEATURE_TYPE extends Feature, SOURCE_TYPE> Index createIndex(fina
         return createIndex(IOUtil.toPath(inputFile), codec, type, null);
     }
 
+    /**
+     * Create a index of the specified type with default binning parameters
+     *
+     * @param inputhPath the input file to load features from
+     * @param codec     the codec to use for decoding records
+     * @param type      the type of index to create
+     */
+    public static <FEATURE_TYPE extends Feature, SOURCE_TYPE> Index createIndex(final Path inputhPath,
+                                                                                final FeatureCodec<FEATURE_TYPE, SOURCE_TYPE> codec,
+                                                                                final IndexType type) {
+        return createIndex(inputhPath, codec, type, null);
+    }
+
+    /**
+     * Create an index of the specified type with default binning parameters
+     *
+     * @param inputFile the input File to load features from
+     * @param codec     the codec to use for decoding records
+     * @param type      the type of index to create
+     * @param sequenceDictionary May be null, but if present may reduce memory footprint for tabix index creation
+     */
+    public static <FEATURE_TYPE extends Feature, SOURCE_TYPE> Index createIndex(final File inputFile,
+                                                                                final FeatureCodec<FEATURE_TYPE, SOURCE_TYPE> codec,
+                                                                                final IndexType type,
+                                                                                final SAMSequenceDictionary sequenceDictionary) {
+        return createIndex(IOUtil.toPath(inputFile), codec, type, sequenceDictionary);
+    }
+
     /**
      * Create an index of the specified type with default binning parameters
      *