MonetDB: bamloader - Keep forward and backward pointers for reve...

[Robin Cijvat]

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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