Changeset: f123faa305d8 for MonetDB
URL: http://dev.monetdb.org/hg/MonetDB?cmd=changeset;node=f123faa305d8
Modified Files:
sql/backends/monet5/bam/bam_loader.c
sql/backends/monet5/bam/bam_wrapper.h
Branch: bamloader
Log Message:
Fixed some memory issues
diffs (100 lines):
diff --git a/sql/backends/monet5/bam/bam_loader.c
b/sql/backends/monet5/bam/bam_loader.c
--- a/sql/backends/monet5/bam/bam_loader.c
+++ b/sql/backends/monet5/bam/bam_loader.c
@@ -571,7 +571,8 @@ bam_loader_files(Client cntxt, MalBlkPtr
char cur;
int line_size;
- size_t line_buf_size = 128;
+ str line = NULL;
+ size_t line_buf_size = 0;
int nr_lines = 1;
str msg = MAL_SUCCEED;
@@ -607,39 +608,35 @@ bam_loader_files(Client cntxt, MalBlkPtr
goto cleanup;
}
/* Enables cleanup to check individual files */
- memset(filenames, 0, sizeof(nr_lines * sizeof(str)));
-
- /* malloc 128 chars for every file; this is safe since call to
- * getline automatically reallocs when buffer is too small */
- for (i = 0; i < nr_lines; ++i) {
- if ((filenames[i] =
- GDKmalloc(line_buf_size * sizeof(char))) == NULL) {
- msg = createException(MAL, "bam_loader_files",
- MAL_MALLOC_FAIL);
- goto cleanup;
- }
- }
+ memset(filenames, 0, nr_lines * sizeof(str));
/* Reset file pointer to beginning of file */
rewind(f);
/* Read BAM filenames into files array */
while ((line_size =
- getline(&filenames[nr_files], &line_buf_size, f)) != -1) {
- str l = filenames[nr_files];
+ getline(&line, &line_buf_size, f)) >= 0) {
- if (l[0] == '\n' || l[0] == '#') {
+ if (line_size == 0 || line[0] == '\n' || line[0] == '\r' ||
line[0] == '#') {
/* Skip empty lines or lines that start with a hash */
+ free(line);
+ line = NULL;
+ /* We need to reset buf size to 0, since getline will
have updated it */
+ line_buf_size = 0;
continue;
}
- if (l[line_size - 1] == '\n') {
+ if (line[line_size - 1] == '\n') {
/* Newline character is not part of the filepath */
- l[line_size - 1] = '\0';
+ line[line_size - 1] = '\0';
}
- ++nr_files;
- /* We need to reset it to 128, since getline might
- * have changed its value */
- line_buf_size = 128;
+ if(line_size > 1 && line[line_size - 2] == '\r') {
+ /* Return character is also not a part of the filepath
*/
+ line[line_size - 2] = '\0';
+ }
+ filenames[nr_files++] = line;
+ line = NULL;
+ /* We need to reset it to 0, since getline will have updated
this val */
+ line_buf_size = 0;
}
if (ferror(f)) {
@@ -661,10 +658,16 @@ bam_loader_files(Client cntxt, MalBlkPtr
nr_threads);
cleanup:
+ if(line) {
+ //if line still contains anything, this is something that was
put there
+ //by getline on the last, failed attempt to read a line
+ free(line);
+ }
+
if (filenames) {
for (i = 0; i < nr_files; ++i) {
if (filenames[i]) {
- GDKfree(filenames[i]);
+ free(filenames[i]);
}
}
GDKfree(filenames);
diff --git a/sql/backends/monet5/bam/bam_wrapper.h
b/sql/backends/monet5/bam/bam_wrapper.h
--- a/sql/backends/monet5/bam/bam_wrapper.h
+++ b/sql/backends/monet5/bam/bam_wrapper.h
@@ -31,7 +31,7 @@
#include <samtools/sam.h>
-#define BW_FP_BUF_SIZE 128
+#define BW_FP_BUF_SIZE 1024
typedef sht ordering;
typedef enum {SAM, BAM} filetype;
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