add function for init-ing search range from single character

TravisWheelerLab · Jan 29, 2024 · 0601107 · 0601107
1 parent 6062d17
commit 0601107
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diff --git a/src/AwFmIndex.h b/src/AwFmIndex.h
@@ -406,6 +406,25 @@ struct AwFmSearchRange awFmCreateInitialQueryRange(
 		const struct AwFmIndex *_RESTRICT_ const index, const char *_RESTRICT_ const query, const uint8_t queryLength);
 
 
+/*
+ * Function:  awFmCreateInitialQueryRangeFromChar
+ * --------------------
+ * Creates the initial Start Pointer - End Pointer range for the given query.
+ *   This is a simpler version of the awFmCreateInitialQueryRange function for when
+ *   you just want to start the range based off a single character
+ *
+ *   NOTE: This function is likely only useful if you need to query on a letter-by-letter
+ *   basis, e.g., to implement inexact matching. If you just want to query for exact matches,
+ *   especially for many queries, use awFmParallelSearchLocate or awFmParallelSearchCount instead.
+ *
+ *  Inputs:
+ *    index: AwFmIndex struct to search
+ *    letter: letter to begin the search with. This will represent the final chacter in a searched kmer.
+ */
+struct AwFmSearchRange awFmCreateInitialQueryRangeFromChar(
+		const struct AwFmIndex *_RESTRICT_ const index, const char letter);
+
+
 /*
  * Function:  awFmIterativeStepBackwardSearch
  * --------------------

diff --git a/src/AwFmSearch.c b/src/AwFmSearch.c
@@ -24,6 +24,23 @@ struct AwFmSearchRange awFmCreateInitialQueryRange(
 }
 
 
+struct AwFmSearchRange awFmCreateInitialQueryRangeFromChar(
+	const struct AwFmIndex *_RESTRICT_ const index, const char letter){
+	uint8_t letterIndex;
+	if(index->config.alphabetType != AwFmAlphabetAmino) {
+		letterIndex = awFmAsciiNucleotideToLetterIndex(letter);
+	}
+	else {
+		letterIndex = awFmAsciiAminoAcidToLetterIndex(letter);
+	}
+	struct AwFmSearchRange searchRange;
+	searchRange.startPtr = index->prefixSums[letterIndex],
+	searchRange.endPtr	 = index->prefixSums[letterIndex + 1] - 1;
+
+	return searchRange;
+}
+
+
 void awFmNucleotideIterativeStepBackwardSearch(
 		const struct AwFmIndex *_RESTRICT_ const index, struct AwFmSearchRange *_RESTRICT_ const range, const uint8_t letter) {