MonetDB: bamloader - Replace sscanf with more efficient parsing ...

[Robin Cijvat]

Changeset: c38437e1b729 for MonetDB
URL: http://dev.monetdb.org/hg/MonetDB?cmd=changeset;node=c38437e1b729
Modified Files:
        sql/backends/monet5/bam/bam_lib.c
Branch: bamloader
Log Message:

Replace sscanf with more efficient parsing in seq_length


diffs (52 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
@@ -183,31 +183,34 @@ reverse_qual(str * ret, str * qual)
        return MAL_SUCCEED;
 }
 
+#define next_cigar_op(fn) { \
+       str tmp; \
+       cnt = strtol(s, &tmp, 10); \
+       if(cnt <= 0 || s == tmp) { \
+               *ret = -1; \
+               throw(MAL, fn, "Could not read CIGAR operation"); \
+       } \
+       s = tmp; \
+       op = *s++; \
+}
+
 str
 seq_length(int * ret, str * cigar)
 {
        int result = 0;
-       str cigar_consumable = *cigar;
+       str s = *cigar;
+       long int cnt;
+       char op;
 
-       if (cigar_consumable[0] == '\0' || 
-                       (cigar_consumable[0] == '*' && cigar_consumable[1] == 
'\0')) {
+       if (*s == '\0' || (*s == '*' && *(s+1) == '\0')) {
                *ret = -1;
                return MAL_SUCCEED;
        }
-       while (cigar_consumable[0] != '\0') {
-               int cnt;
-               char op;
-               int nr_chars_read;
-
-               if (sscanf
-                       (cigar_consumable, "%d%c%n", &cnt, &op,
-                        &nr_chars_read) != 2)
-                       throw(MAL, "seq_length",
-                                 "Error parsing CIGAR string '%s'\n", *cigar);
+       while (*s != '\0') {
+               next_cigar_op("seq_length");
                if (op == 'M' || op == 'D' || op == 'N' || op == '='
                        || op == 'X')
                        result += cnt;
-               cigar_consumable += nr_chars_read;
        }
        *ret = result;
        return MAL_SUCCEED;
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