Merge pull request #16 from TravisWheelerLab/constGetHeaderSeq

change FV struct to const when getting sequence/header
TravisWheelerLab · Mar 16, 2024 · 7ac0534 · 7ac0534
2 parents c86ef63 + 948f652
commit 7ac0534
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Showing 5 changed files with 15 additions and 14 deletions.
diff --git a/src/FastaVector.c b/src/FastaVector.c
@@ -293,8 +293,9 @@ fastaVectorAddSequenceToList(struct FastaVector *fastaVector, char *header,
 
 // return NULL for headerPtr and 0 for header length if the fastaVector does not
 // have a header for the given headerIndex
-void fastaVectorGetHeader(struct FastaVector *fastaVector, size_t headerIndex,
-                          char **headerPtr, size_t *headerLength) {
+void fastaVectorGetHeader(const struct FastaVector *const fastaVector,
+                          size_t headerIndex, char **headerPtr,
+                          size_t *headerLength) {
   if (__builtin_expect(headerIndex >= fastaVector->metadata.count, false)) {
     *headerLength = 0;
     *headerPtr = NULL;
@@ -314,7 +315,7 @@ void fastaVectorGetHeader(struct FastaVector *fastaVector, size_t headerIndex,
 
 // return NULL for headerPtr and 0 for header length if the fastaVector does not
 // have a header for the given headerIndex
-void fastaVectorGetSequence(struct FastaVector *fastaVector,
+void fastaVectorGetSequence(const struct FastaVector *const fastaVector,
                             size_t sequenceIndex, char **sequencePtr,
                             size_t *sequenceLength) {
   if (__builtin_expect(sequenceIndex >= fastaVector->metadata.count, false)) {

diff --git a/src/FastaVector.h b/src/FastaVector.h
@@ -162,8 +162,9 @@ fastaVectorAddSequenceToList(struct FastaVector *fastaVector, char *header,
  *
  *
  */
-void fastaVectorGetHeader(struct FastaVector *fastaVector, size_t headerIndex,
-                          char **headerPtr, size_t *headerLength);
+void fastaVectorGetHeader(const struct FastaVector *const fastaVector,
+                          size_t headerIndex, char **headerPtr,
+                          size_t *headerLength);
 
 /**
  * @relates FastaVector
@@ -180,7 +181,7 @@ void fastaVectorGetHeader(struct FastaVector *fastaVector, size_t headerIndex,
  * TODO: Should we return a static code in case the index was out of bounds?
  *
  */
-void fastaVectorGetSequence(struct FastaVector *fastaVector,
+void fastaVectorGetSequence(const struct FastaVector *const fastaVector,
                             size_t sequenceIndex, char **sequencePtr,
                             size_t *sequenceLength);
 

diff --git a/tests/fileReadTest/fileReadTest.c b/tests/fileReadTest/fileReadTest.c
@@ -18,8 +18,7 @@ void readTest(char **const testHeaderStrings, char **const testSequenceStrings,
                    "fail on reading test1.fasta for test 1");
 
   for (size_t i = 0; i < numHeaders; i++) {
-    // add 1 to the strings for the  null terminators
-    const size_t expectedHeaderLength = strlen(testHeaderStrings[i]) + 1;
+    const size_t expectedHeaderLength = strlen(testHeaderStrings[i]);
     const size_t expectedSequenceLength = strlen(testSequenceStrings[i]);
     size_t headerLength;
     char *headerPtr;
@@ -51,7 +50,7 @@ void readTest(char **const testHeaderStrings, char **const testSequenceStrings,
             testSequenceStrings[i], (int)sequenceLength, sequencePtr);
     testAssertString(stringsMatch, buffer);
 
-    char terminator = headerPtr[headerLength - 1];
+    char terminator = headerPtr[headerLength];
     sprintf(buffer,
             "header index %zu was not null terminated! (found char %u after "
             "the end of the header)",

diff --git a/tests/fileWriteTest/fileWriteTest.c b/tests/fileWriteTest/fileWriteTest.c
@@ -111,9 +111,9 @@ void fastaVectorFileWriteTest(const size_t numSequences, const char *fileSrc) {
     size_t headerLengthFromVector;
     size_t sequenceLengthFromVector;
     fastaVectorGetHeader(&fastaVector, sequenceNum, &headerFromVector,
-                              &headerLengthFromVector);
+                         &headerLengthFromVector);
     fastaVectorGetSequence(&fastaVector, sequenceNum, &sequenceFromVector,
-                                &sequenceLengthFromVector);
+                           &sequenceLengthFromVector);
     sprintf(buffer, "header was supposed to be length %zu, but got %zu.",
             headerLength, headerLengthFromVector);
     testAssertString((headerLength + 1) == headerLengthFromVector, buffer);
@@ -156,7 +156,7 @@ void fastaVectorFileWriteTest(const size_t numSequences, const char *fileSrc) {
     size_t lastHeaderLen;
     char *lastHeaderPtr;
     fastaVectorGetHeader(&fastaVector, fastaVector.metadata.count - 1,
-                              &lastHeaderPtr, &lastHeaderLen);
+                         &lastHeaderPtr, &lastHeaderLen);
     printf("headers did not match, \n h1: %.*s\n h2: %.*s\n hr: %.*s\n",
            (int)fastaVector.header.count, fastaVector.header.charData,
            (int)fastaReadVector.header.count, fastaReadVector.header.charData,

diff --git a/tests/multiSequenceTest/multiSequenceTest.c b/tests/multiSequenceTest/multiSequenceTest.c
@@ -24,12 +24,12 @@ int main() {
   for (uint8_t i = 0; i < 6; i++) {
     size_t length;
     char *charPtr;
-    fastaVectorFastaGetHeader(&fastaVector, i, &charPtr, &length);
+    fastaVectorGetHeader(&fastaVector, i, &charPtr, &length);
     testAssertString(length == strlen(headers[i]),
                      "header lengths did not match");
     testAssertString(strcmp(headers[i], charPtr) == 0,
                      "headers did not match exactly.");
-    fastaVectorFastaGetSequence(&fastaVector, i, &charPtr, &length);
+    fastaVectorGetSequence(&fastaVector, i, &charPtr, &length);
     testAssertString(length == strlen(seqs[i]),
                      "sequence lengths did not match");
     testAssertString(strcmp(seqs[i], charPtr) == 0,