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fix memory leak in SamRecord::setTagsFromBuffer() #28

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fix memory leak in SamRecord::setTagsFromBuffer() #28

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124 changes: 61 additions & 63 deletions bam/SamRecord.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -3018,33 +3018,31 @@ bool SamRecord::setTagsFromBuffer()

// First check if the tag already exists.
unsigned int location = extras.Find(key);
int origIndex = 0;
String* duplicate = NULL;
String* origTag = NULL;
int origIndex = -1;
String duplicate;
String origTag;
if(location != LH_NOTFOUND)
{
duplicate = new String;
origTag = new String;
origIndex = extras[location];

*duplicate = (char)(extraPtr[0]);
*duplicate += (char)(extraPtr[1]);
*duplicate += ':';
duplicate = (char)(extraPtr[0]);
duplicate += (char)(extraPtr[1]);
duplicate += ':';

*origTag = *duplicate;
*duplicate += (char)(extraPtr[2]);
*duplicate += ':';
origTag = duplicate;
duplicate += (char)(extraPtr[2]);
duplicate += ':';
}

switch (extraPtr[2])
{
case 'A' :
if(duplicate != NULL)
if(location != LH_NOTFOUND)
{
*duplicate += (* (char *) content);
*origTag += intType[origIndex];
*origTag += ':';
appendIntArrayValue(origIndex, *origTag);
duplicate += (* (char *) content);
origTag += intType[origIndex];
origTag += ':';
appendIntArrayValue(origIndex, origTag);
tagBufferSize -= getNumericTagTypeSize(intType[origIndex]);
integers[origIndex] = *(char *)content;
intType[origIndex] = extraPtr[2];
Expand All @@ -3060,12 +3058,12 @@ bool SamRecord::setTagsFromBuffer()
extraPtr += 4;
break;
case 'c' :
if(duplicate != NULL)
if(location != LH_NOTFOUND)
{
*duplicate += (* (char *) content);
*origTag += intType[origIndex];
*origTag += ':';
appendIntArrayValue(origIndex, *origTag);
duplicate += (* (char *) content);
origTag += intType[origIndex];
origTag += ':';
appendIntArrayValue(origIndex, origTag);
tagBufferSize -= getNumericTagTypeSize(intType[origIndex]);
integers[origIndex] = *(char *)content;
intType[origIndex] = extraPtr[2];
Expand All @@ -3081,12 +3079,12 @@ bool SamRecord::setTagsFromBuffer()
extraPtr += 4;
break;
case 'C' :
if(duplicate != NULL)
if(location != LH_NOTFOUND)
{
*duplicate += (* (unsigned char *) content);
*origTag += intType[origIndex];
*origTag += ':';
appendIntArrayValue(origIndex, *origTag);
duplicate += (* (unsigned char *) content);
origTag += intType[origIndex];
origTag += ':';
appendIntArrayValue(origIndex, origTag);
tagBufferSize -= getNumericTagTypeSize(intType[origIndex]);
integers[origIndex] = *(unsigned char *)content;
intType[origIndex] = extraPtr[2];
Expand All @@ -3102,12 +3100,12 @@ bool SamRecord::setTagsFromBuffer()
extraPtr += 4;
break;
case 's' :
if(duplicate != NULL)
if(location != LH_NOTFOUND)
{
*duplicate += (* (short *) content);
*origTag += intType[origIndex];
*origTag += ':';
appendIntArrayValue(origIndex, *origTag);
duplicate += (* (short *) content);
origTag += intType[origIndex];
origTag += ':';
appendIntArrayValue(origIndex, origTag);
tagBufferSize -= getNumericTagTypeSize(intType[origIndex]);
integers[origIndex] = *(short *)content;
intType[origIndex] = extraPtr[2];
Expand All @@ -3123,12 +3121,12 @@ bool SamRecord::setTagsFromBuffer()
extraPtr += 5;
break;
case 'S' :
if(duplicate != NULL)
if(location != LH_NOTFOUND)
{
*duplicate += (* (unsigned short *) content);
*origTag += intType[origIndex];
*origTag += ':';
appendIntArrayValue(origIndex, *origTag);
duplicate += (* (unsigned short *) content);
origTag += intType[origIndex];
origTag += ':';
appendIntArrayValue(origIndex, origTag);
tagBufferSize -= getNumericTagTypeSize(intType[origIndex]);
integers[origIndex] = *(unsigned short *)content;
intType[origIndex] = extraPtr[2];
Expand All @@ -3144,12 +3142,12 @@ bool SamRecord::setTagsFromBuffer()
extraPtr += 5;
break;
case 'i' :
if(duplicate != NULL)
if(location != LH_NOTFOUND)
{
*duplicate += (* (int *) content);
*origTag += intType[origIndex];
*origTag += ':';
appendIntArrayValue(origIndex, *origTag);
duplicate += (* (int *) content);
origTag += intType[origIndex];
origTag += ':';
appendIntArrayValue(origIndex, origTag);
tagBufferSize -= getNumericTagTypeSize(intType[origIndex]);
integers[origIndex] = *(int *)content;
intType[origIndex] = extraPtr[2];
Expand All @@ -3165,12 +3163,12 @@ bool SamRecord::setTagsFromBuffer()
extraPtr += 7;
break;
case 'I' :
if(duplicate != NULL)
if(location != LH_NOTFOUND)
{
*duplicate += (* (unsigned int *) content);
*origTag += intType[origIndex];
*origTag += ':';
appendIntArrayValue(origIndex, *origTag);
duplicate += (* (unsigned int *) content);
origTag += intType[origIndex];
origTag += ':';
appendIntArrayValue(origIndex, origTag);
tagBufferSize -= getNumericTagTypeSize(intType[origIndex]);
integers[origIndex] = *(unsigned int *)content;
intType[origIndex] = extraPtr[2];
Expand All @@ -3186,12 +3184,12 @@ bool SamRecord::setTagsFromBuffer()
extraPtr += 7;
break;
case 'Z' :
if(duplicate != NULL)
if(location != LH_NOTFOUND)
{
*duplicate += ((const char *) content);
*origTag += 'Z';
*origTag += ':';
*origTag += (char*)(strings[origIndex]);
duplicate += ((const char *) content);
origTag += 'Z';
origTag += ':';
origTag += (char*)(strings[origIndex]);
tagBufferSize -= strings[origIndex].Length();
strings[origIndex] = (const char *) content;
extraPtr += 4 + strings[origIndex].Length();
Expand All @@ -3206,17 +3204,17 @@ bool SamRecord::setTagsFromBuffer()
}
break;
case 'B' :
if(duplicate != NULL)
if(location != LH_NOTFOUND)
{
*origTag += 'B';
*origTag += ':';
*origTag += (char*)(strings[origIndex]);
origTag += 'B';
origTag += ':';
origTag += (char*)(strings[origIndex]);
tagBufferSize -=
getBtagBufferSize(strings[origIndex]);
int bufferSize =
getStringFromBtagBuffer((unsigned char*)content,
strings[origIndex]);
*duplicate += (char *)(strings[origIndex]);
duplicate += (char *)(strings[origIndex]);
tagBufferSize += bufferSize;
extraPtr += 3 + bufferSize;
}
Expand All @@ -3233,12 +3231,12 @@ bool SamRecord::setTagsFromBuffer()
}
break;
case 'f' :
if(duplicate != NULL)
if(location != LH_NOTFOUND)
{
duplicate->appendFullFloat(* (float *) content);
*origTag += 'f';
*origTag += ':';
origTag->appendFullFloat(floats[origIndex]);
duplicate.appendFullFloat(* (float *) content);
origTag += 'f';
origTag += ':';
origTag.appendFullFloat(floats[origIndex]);
floats[origIndex] = *(float *)content;
}
else
Expand Down Expand Up @@ -3275,15 +3273,15 @@ bool SamRecord::setTagsFromBuffer()
status = false;
}

if(duplicate != NULL)
if(location != LH_NOTFOUND)
{
// Duplicate tag in this record.
// Tag already existed, print message about overwriting.
// WARN about dropping duplicate tags.
if(myNumWarns++ < myMaxWarns)
{
fprintf(stderr, "WARNING: Duplicate Tags, overwritting %s with %s\n",
origTag->c_str(), duplicate->c_str());
origTag.c_str(), duplicate.c_str());
if(myNumWarns == myMaxWarns)
{
fprintf(stderr, "Suppressing rest of Duplicate Tag warnings.\n");
Expand Down