update formatting to split else clause onto next line after brace

src/AwFmFile.c

@@ -315,7 +315,8 @@ enum AwFmReturnCode awFmReadIndexFromFile(
 			fclose(fileHandle);
 			awFmDeallocIndex(indexData);
 			return AwFmAllocationFailure;
-		} else {
+		}
+		else {
 			elementsRead = fread(indexData->suffixArray.values, 1, compressedSuffixArrayByteLength, fileHandle);
 			if(elementsRead != compressedSuffixArrayByteLength) {
 				fclose(fileHandle);
@@ -408,8 +409,8 @@ enum AwFmReturnCode awFmReadSequenceFromFile(const struct AwFmIndex *restrict co
 		// null terminate the string
 		sequenceBuffer[sequenceSegmentLength] = 0;
 		return AwFmFileReadOkay;
-
-	} else {
+	}
+	else {
 
 		return AwFmUnsupportedVersionError;
 	}
@@ -467,7 +468,8 @@ size_t awFmGetSequenceFileOffset(const struct AwFmIndex *restrict const index) {
 size_t awFmGetSuffixArrayFileOffset(const struct AwFmIndex *restrict const index) {
 	if(index->config.storeOriginalSequence) {
 		return awFmGetSequenceFileOffset(index) + ((index->bwtLength - 1) * sizeof(char));
-	} else {
+	}
+	else {
 		return awFmGetSequenceFileOffset(index);
 	}
 }

src/AwFmKmerTable.c

@@ -92,7 +92,8 @@ static inline struct AwFmSearchRange awFmNucleotidePartialKmerSeedRangeFromTable
 	if(__builtin_expect((kmer[kmerLength - 1] | 0x20) == 't', 0)) {
 		// lookup kmer from scratch
 		awFmNucleotideNonSeededSearch(index, kmer, kmerLength, &range);
-	} else {
+	}
+	else {
 
 		const uint64_t endSequenceKmerTableIndex = 0;	 // index->endSequenceKmerTableIndex;
 		const uint8_t kmerLengthInSeedTable			 = index->config.kmerLengthInSeedTable;
@@ -141,7 +142,8 @@ inline struct AwFmSearchRange awFmAminoPartialKmerSeedRangeFromTable(
 	if(__builtin_expect((kmer[kmerLength - 1] | 0x20) == 'y', 0)) {
 		// lookup kmer from scratch
 		awFmAminoNonSeededSearch(index, kmer, kmerLength, &range);
-	} else {
+	}
+	else {
 
 		const uint64_t endSequenceKmerTableIndex = 0;	 // index->endSequenceKmerTableIndex;
 		const uint8_t kmerLengthInSeedTable			 = index->config.kmerLengthInSeedTable;

src/AwFmLetter.c

@@ -47,7 +47,8 @@ uint8_t awFmNucleotideCompressedVectorToLetterIndex(const uint8_t compressedVect
 uint8_t awFmAsciiAminoAcidToLetterIndex(const uint8_t asciiLetter) {
 	if(__builtin_expect(asciiLetter == '$', 0)) {
 		return 21;
-	} else {
+	}
+	else {
 		static const uint8_t letterEncodings[32] = {20, 0, 20, 1, 2, 3, 4, 5, 6, 7, 20, 8, 9, 10, 11, 20, 12, 13, 14, 15,
 				16, 20, 17, 18, 20, 19, 20, 20, 20, 20, 20, 20};
 		// find the index and mod (to prevent array out of bounds for weird ascii inputs)
@@ -63,7 +64,8 @@ uint8_t awFmAsciiAminoLetterSanitize(const uint8_t asciiLetter) {
 
 	if(__builtin_expect(letterIsAmbiguityChar, 0)) {
 		return 'z';
-	} else {
+	}
+	else {
 		return asciiLetter;
 	}
 }

src/AwFmParallelSearch.c

@@ -108,7 +108,8 @@ void awFmParallelSearchLocate(const struct AwFmIndex *restrict const index,
 			parallelSearchExtendKmersInBlock(index, searchList, ranges, threadBlockStartIndex, threadBlockEndIndex);
 			parallelSearchTracebackPositionLists(index, searchList, ranges, threadBlockStartIndex, threadBlockEndIndex);
 		}
-	} else {
+	}
+	else {
 		// exact duplicate of above code, without the omp pragma, so it doesn't kill performance with only 1 thread.
 		for(size_t threadBlockStartIndex = 0; threadBlockStartIndex < searchListCount;
 				threadBlockStartIndex += AW_FM_NUM_CONCURRENT_QUERIES) {
@@ -147,7 +148,8 @@ void awFmParallelSearchCount(const struct AwFmIndex *restrict const index,
 				searchList->kmerSearchData[i].count = awFmSearchRangeLength(&ranges[i - threadBlockStartIndex]);
 			}
 		}
-	} else {
+	}
+	else {
 		// exact duplicate of above code, without the omp pragma, so it doesn't kill performance with only 1 thread.
 		for(size_t threadBlockStartIndex = 0; threadBlockStartIndex < searchListCount;
 				threadBlockStartIndex += AW_FM_NUM_CONCURRENT_QUERIES) {
@@ -183,14 +185,16 @@ void parallelSearchFindKmerSeedsForBlock(const struct AwFmIndex *restrict const
 			// TODO: reimplement partial seeded search when it's implementable
 			if(kmerLength < index->config.kmerLengthInSeedTable) {
 				awFmNucleotideNonSeededSearch(index, kmerString, kmerLength, &ranges[rangesIndex]);
-			} else {
+			}
+			else {
 				ranges[rangesIndex] = awFmNucleotideKmerSeedRangeFromTable(index, kmerString, kmerLength);
 			}
-		} else {
+		}
+		else {
 			if(kmerLength < index->config.kmerLengthInSeedTable) {
 				awFmAminoNonSeededSearch(index, kmerString, kmerLength, &ranges[rangesIndex]);
-
-			} else {
+			}
+			else {
 				ranges[rangesIndex] = awFmAminoKmerSeedRangeFromTable(index, kmerString, kmerLength);
 			}
 		}
@@ -221,7 +225,8 @@ void parallelSearchExtendKmersInBlock(const struct AwFmIndex *restrict const ind
 				if(index->config.alphabetType == AwFmAlphabetNucleotide) {
 					const uint8_t queryLetterIndex = awFmAsciiNucleotideToLetterIndex(kmerString[currentQueryLetterIndex]);
 					awFmNucleotideIterativeStepBackwardSearch(index, &ranges[rangesIndex], queryLetterIndex);
-				} else {
+				}
+				else {
 					const uint8_t queryLetterIndex = awFmAsciiAminoAcidToLetterIndex(kmerString[currentQueryLetterIndex]);
 					awFmAminoIterativeStepBackwardSearch(index, &ranges[rangesIndex], queryLetterIndex);
 				}
@@ -256,7 +261,8 @@ void parallelSearchTracebackPositionLists(const struct AwFmIndex *restrict const
 					backtrace.position = awFmNucleotideBacktraceBwtPosition(index, backtrace.position);
 					backtrace.offset++;
 				}
-			} else {
+			}
+			else {
 				while(!awFmBwtPositionIsSampled(index, backtrace.position)) {
 					backtrace.position = awFmAminoBacktraceBwtPosition(index, backtrace.position);
 					backtrace.offset++;
@@ -273,7 +279,8 @@ void parallelSearchTracebackPositionLists(const struct AwFmIndex *restrict const
 bool setPositionListCount(struct AwFmKmerSearchData *restrict const searchData, uint32_t newCount) {
 	if(__builtin_expect(searchData->capacity >= newCount, 1)) {
 		searchData->count = newCount;
-	} else {
+	}
+	else {
 		const size_t newCapacity			= newCount;
 		const size_t newLengthInBytes = newCapacity * sizeof(uint64_t);
 		void *tmpPtr									= realloc(searchData->positionList, newLengthInBytes);

src/AwFmSearch.c

@@ -11,7 +11,8 @@ struct AwFmSearchRange awFmCreateInitialQueryRange(
 	uint8_t finalLetterIndexInQuery;
 	if(index->config.alphabetType == AwFmAlphabetNucleotide) {
 		finalLetterIndexInQuery = awFmAsciiNucleotideToLetterIndex(query[queryLength - 1]);
-	} else {
+	}
+	else {
 		finalLetterIndexInQuery = awFmAsciiAminoAcidToLetterIndex(query[queryLength - 1]);
 	}
 
@@ -167,7 +168,8 @@ uint64_t *awFmFindDatabaseHitPositions(const struct AwFmIndex *restrict const in
 				backtracePosition = awFmNucleotideBacktraceBwtPosition(index, backtracePosition);
 				databaseSequenceOffset++;
 			}
-		} else {
+		}
+		else {
 			while(!awFmBwtPositionIsSampled(index, backtracePosition)) {
 				backtracePosition = awFmAminoBacktraceBwtPosition(index, backtracePosition);
 				databaseSequenceOffset++;
@@ -203,7 +205,8 @@ enum AwFmReturnCode awFmGetLocalSequencePositionFromIndexPosition(const struct A
 		size_t globalPosition, size_t *sequenceNumber, size_t *localSequencePosition) {
 	if(!index->fastaVector) {
 		return AwFmUnsupportedVersionError;
-	} else {
+	}
+	else {
 		if(globalPosition >= index->bwtLength) {
 			return AwFmIllegalPositionError;
 		}
@@ -216,7 +219,8 @@ enum AwFmReturnCode awFmGetLocalSequencePositionFromIndexPosition(const struct A
 				size_t sequenceStartPosition;
 				if(sequenceIndex == 0) {
 					sequenceStartPosition = 0;
-				} else {
+				}
+				else {
 					sequenceStartPosition = index->fastaVector->metadata.data[sequenceIndex - 1].sequenceEndPosition;
 				}
 				*sequenceNumber				 = sequenceIndex;
@@ -257,7 +261,8 @@ struct AwFmSearchRange awFmDatabaseSingleKmerExactMatch(
 	if(index->config.alphabetType == AwFmAlphabetNucleotide) {
 		bwtBlockWidth		= sizeof(struct AwFmNucleotideBlock);
 		kmerLetterIndex = awFmAsciiNucleotideToLetterIndex(kmer[kmerLetterPosition]);
-	} else {
+	}
+	else {
 		bwtBlockWidth		= sizeof(struct AwFmAminoBlock);
 		kmerLetterIndex = awFmAsciiAminoAcidToLetterIndex(kmer[kmerLetterPosition]);
 	}
@@ -273,7 +278,8 @@ struct AwFmSearchRange awFmDatabaseSingleKmerExactMatch(
 			kmerLetterIndex = awFmAsciiNucleotideToLetterIndex(kmer[kmerLetterPosition]);
 			awFmNucleotideIterativeStepBackwardSearch(index, &range, kmerLetterIndex);
 		}
-	} else {
+	}
+	else {
 		while(__builtin_expect(awFmSearchRangeIsValid(&range) && (kmerLetterPosition--), 1)) {
 			kmerLetterIndex = awFmAsciiAminoAcidToLetterIndex(kmer[kmerLetterPosition]);
 			awFmAminoIterativeStepBackwardSearch(index, &range, kmerLetterIndex);

src/AwFmSuffixArray.c

@@ -137,7 +137,8 @@ enum AwFmReturnCode awFmReadPositionsFromSuffixArray(const struct AwFmIndex *res
 		}
 
 		return AwFmSuccess;
-	} else {
+	}
+	else {
 		for(size_t i = 0; i < positionArrayLength; i++) {
 			size_t indexInSuffixArray = positionArray[i] / index->config.suffixArrayCompressionRatio;
 			enum AwFmReturnCode rc		= awFmGetSuffixArrayValueFromFile(index, indexInSuffixArray, &positionArray[i]);
@@ -160,8 +161,8 @@ enum AwFmReturnCode awFmSuffixArrayReadPositionParallel(
 		size_t saValue				 = awFmGetValueFromCompressedSuffixArray(&index->suffixArray, suffixArrayPosition);
 		backtracePtr->position = (saValue + backtracePtr->offset) % index->bwtLength;
 		return AwFmSuccess;
-
-	} else {
+	}
+	else {
 		uint64_t suffixArrayPosition = backtracePtr->position / index->config.suffixArrayCompressionRatio;
 		size_t saValue;
 		enum AwFmReturnCode rc = awFmGetSuffixArrayValueFromFile(index, suffixArrayPosition, &saValue);

test/kmerSeedTableTests/kmerSeedTableTests.c

@@ -74,7 +74,8 @@ void checkRangeForCorrectness(const struct AwFmSearchRange *restrict const range
 
 			sprintf(buffer, "range had position %zu for kmer %s, but that position holds kmer %s.\n", position, kmerBuffer,
 					sequenceBuffer);
-		} else {
+		}
+		else {
 			sprintf(buffer, "position %zu matches kmer %s, but was not represented in the range.\n", position, kmerBuffer);
 		}
 		testAssertString((kmerFoundAtPosition == positionFoundInRange), buffer);
@@ -160,7 +161,8 @@ void testAllKmerRanges(struct AwFmIndexConfiguration *config, uint64_t sequenceL
 		char *kmer2									 = "agaaa";
 		if(config->alphabetType == AwFmAlphabetNucleotide) {
 			awFmNucleotideNonSeededSearch(index, kmer2, 5, &range);
-		} else {
+		}
+		else {
 			awFmAminoNonSeededSearch(index, kmer2, 5, &range);
 		}
 		printf("range for agaaa: %zu, %zu\n", range.startPtr, range.endPtr);
@@ -193,7 +195,8 @@ void testAllKmerRanges(struct AwFmIndexConfiguration *config, uint64_t sequenceL
 				if(index->config.alphabetType == AwFmAlphabetNucleotide) {
 					kmer[letterInKmer] = nucleotideLookup[(kmerIndexCopy % 4)];
 					kmerIndexCopy /= 4;
-				} else {
+				}
+				else {
 					kmer[letterInKmer] = aminoLookup[(kmerIndexCopy % 20)];
 					kmerIndexCopy /= 20;
 				}

test/multiSequenceIndexTest/AwFmMultiSequenceTest.c

@@ -318,14 +318,16 @@ void testAwFmIndexGivesCorrectHeaders(void) {
 			char *headerBufferPtrFromFastaVector;
 			if(sequenceIndex == 0) {
 				headerBufferPtrFromFastaVector = fastaVector->header.charData;
-			} else {
+			}
+			else {
 				size_t headerOffset						 = fastaVector->metadata.data[sequenceIndex - 1].headerEndPosition;
 				headerBufferPtrFromFastaVector = fastaVector->header.charData + headerOffset;
 			}
 			size_t headerLengthFromFastaVector;
 			if(sequenceIndex == 0) {
 				headerLengthFromFastaVector = fastaVector->metadata.data[0].headerEndPosition;
-			} else {
+			}
+			else {
 				size_t startPosition				= fastaVector->metadata.data[sequenceIndex - 1].headerEndPosition;
 				size_t endPosition					= fastaVector->metadata.data[sequenceIndex].headerEndPosition;
 				headerLengthFromFastaVector = endPosition - startPosition;
@@ -411,7 +413,8 @@ void compareIndicesForEqualityIgnoreVersion(const struct AwFmIndex *index1, cons
 					}
 				}
 			}
-		} else {
+		}
+		else {
 			bool blocksAreEqual = memcmp(&index1->bwtBlockList.asAmino[blockIndex], &index2->bwtBlockList.asAmino[blockIndex],
 																sizeof(struct AwFmAminoBlock)) == 0;
 			sprintf(buffer, "index 1 bwt block %zu did not compare equal to matching index 2 block.", blockIndex);

test/occupancyPerformanceTest/occSpeedTest.c

@@ -71,7 +71,8 @@ void performDbQueries(const struct AwFmIndex *restrict const index, uint64_t pos
 			ptrs[1] = ptrs[1] % positionsInDb;
 			awFmOccupancyDataPrefetch(index, ptrs[1]);
 		}
-	} else {
+	}
+	else {
 		for(uint32_t i = 0; i < numQueries; i++) {
 			uint8_t letter = rand() % 20;
 			ptrs[0]				 = awFmGetOccupancy(index, ptrs[0], letter) + index->rankPrefixSums[letter];

test/parallelSearch/parallelSearchTest.c

@@ -161,7 +161,8 @@ void testParallelSearchAmino(void) {
 							sequence + sequencePosition, sequencePosition);
 					testAssertString(false, buffer);
 					exit(-1);
-				} else if(!kmerFoundAtThisPosition && thisPositionInList) {
+				}
+				else if(!kmerFoundAtThisPosition && thisPositionInList) {
 					printf("kmer %zu has count %u\n", kmerIndex, searchData->count);
 					printf("position list: ");
 					for(size_t i = 0; i < searchData->count; i++) {
@@ -296,7 +297,8 @@ void testParallelSearchNucleotide() {
 
 					testAssertString(false, buffer);
 					exit(-2);
-				} else if(!kmerFoundAtThisPosition && thisPositionInList) {
+				}
+				else if(!kmerFoundAtThisPosition && thisPositionInList) {
 					printf("kmer %zu has count %u\n", kmerIndex, searchData->count);
 					printf("position list: ");
 					for(size_t i = 0; i < searchData->count; i++) {

test/searchTest/searchTest.c

@@ -84,7 +84,8 @@ void generateRandomIndex(struct AwFmIndex **index, uint8_t **sequence, size_t se
 	if(sequence == NULL) {
 		printf("critical failure: could not allocate sequence in unit test.");
 		exit(-1);
-	} else if(suffixArray == NULL) {
+	}
+	else if(suffixArray == NULL) {
 		printf("critical failure: could not allocate suffix array in unit test.");
 		exit(-2);
 	}
@@ -162,8 +163,8 @@ void testRangeForCorrectness(const struct AwFmSearchRange *range, const uint8_t
 				printf("%zu, ", suffixArray[i]);
 			}
 			printf("]\n");
-
-		} else if(!kmerFoundAtPosition && kmerExpectedAtPosition) {
+		}
+		else if(!kmerFoundAtPosition && kmerExpectedAtPosition) {
 			sprintf(buffer,
 					"kmer  \"%.*s\" returned range [%zu, %zu], which contains position %zu, but that position was not in range:",
 					kmerLength, kmer, range->startPtr, range->endPtr, position);

tuning/build/buildIndex.c

@@ -55,7 +55,8 @@ int main(int argc, char **argv) {
 	if(chromosomeNumber == -1 && !fullGenomeIndexRequested) {
 		printf("no chromosome or full genome specified, defaulting to chromosome 21.\n");
 		chromosomeNumber = 21;
-	} else if(chromosomeNumber != -1 && fullGenomeIndexRequested) {
+	}
+	else if(chromosomeNumber != -1 && fullGenomeIndexRequested) {
 		printf(
 				"the full genome flag was set, but a specific chromosome was also requested. Ignoring full genome and making "
 				"index on chromosome %i\n",
@@ -67,7 +68,8 @@ int main(int argc, char **argv) {
 	// build the index using the parsed settings
 	if(fullGenomeIndexRequested) {
 		buildFullGenomeIndex(suffixArrayCompressionRatio, kmerLengthInSeedTable, indexFilenameBuffer);
-	} else {
+	}
+	else {
 		buildChromosomeIndex(chromosomeNumber, suffixArrayCompressionRatio, kmerLengthInSeedTable, indexFilenameBuffer);
 	}
 }
@@ -111,8 +113,8 @@ void buildChromosomeIndex(
 	if(sequenceLength > 1000) {
 		printf("for reference, here's the first 1000 characters in the sequence: %.*s\n", 1000, sequenceBuffer);
 		printf("...and the last 10 characters: %.*s\n", 10, &sequenceBuffer[sequenceLength - 10]);
-
-	} else {
+	}
+	else {
 		printf("for reference, here's all %zu characters in the sequence: %.*s\n", sequenceLength, (int)sequenceLength,
 				sequenceBuffer);
 	}

tuning/search/timeSearch.c

@@ -70,7 +70,8 @@ int main(int argc, char **argv) {
 		// search for the kmers
 		if(useCountFunction) {
 			awFmParallelSearchCount(index, searchList, numThreadsInParallelQuery);
-		} else {
+		}
+		else {
 			awFmParallelSearchLocate(index, searchList, numThreadsInParallelQuery);
 		}
 		clock_t searchEndTime			= clock();
@@ -128,7 +129,8 @@ bool charIsAmbiguous(char c, enum AwFmAlphabetType alphabet) {
 				return false;
 			}
 		}
-	} else {
+	}
+	else {
 		for(uint8_t i = 0; i < 20; i++) {
 			if(tolower(c) == aminoLookup[i]) {
 				return false;
@@ -167,7 +169,8 @@ bool getStringFromSequenceFile(
 		if(charFromFile >= 'A' && charFromFile < 'z') {
 			if(charIsAmbiguous(charFromFile, alphabet)) {
 				return false;
-			} else {
+			}
+			else {
 				buffer[charactersGrabbed++] = charFromFile;
 			}
 		}