Changeset: 86ac986f6f30 for MonetDB
URL: http://dev.monetdb.org/hg/MonetDB?cmd=changeset;node=86ac986f6f30
Modified Files:
sql/backends/monet5/bam/bam_lib.c
Branch: bamloader
Log Message:
Keep forward and backward pointers for reverse_seq and reverse_qual to improve
performance
diffs (46 lines):
diff --git a/sql/backends/monet5/bam/bam_lib.c
b/sql/backends/monet5/bam/bam_lib.c
--- a/sql/backends/monet5/bam/bam_lib.c
+++ b/sql/backends/monet5/bam/bam_lib.c
@@ -141,17 +141,21 @@ reverse_seq(str * ret, str * seq)
unsigned int i;
unsigned int len = strlen(*seq);
sht map_index;
+ str forward = *seq;
+ str backward;
result = GDKmalloc((len + 1) * sizeof(char));
if (result == NULL)
throw(MAL, "reverse_seq", MAL_MALLOC_FAIL);
+ backward = &result[len-1];
for (i = 0; i < len; ++i) {
- map_index = (sht)((*seq)[i] - 'A');
+ map_index = (sht)(*forward++ - 'A');
if(map_index < 0 || map_index > 24 ||
- (result[len - i - 1] =
reverse_seq_map[map_index]) == 0) {
- result[len - i - 1] = '?';
+ (*backward = reverse_seq_map[map_index]) == 0) {
+ *backward = '?';
}
+ --backward;
}
result[len] = '\0';
*ret = result;
@@ -164,12 +168,16 @@ reverse_qual(str * ret, str * qual)
str result;
unsigned int i;
unsigned int len = strlen(*qual);
+ str forward = *qual;
+ str backward;
result = GDKmalloc((len + 1) * sizeof(char));
if (result == NULL)
throw(MAL, "reverse_qual", MAL_MALLOC_FAIL);
+
+ backward = &result[len-1];
for (i = 0; i < len; ++i)
- result[len - i - 1] = (*qual)[i];
+ *backward-- = *forward++;
result[len] = '\0';
*ret = result;
return MAL_SUCCEED;
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