Changeset: 5b5cbb2c5217 for MonetDB
URL: http://dev.monetdb.org/hg/MonetDB?cmd=changeset;node=5b5cbb2c5217
Modified Files:
sql/backends/monet5/bam/bam_lib.c
Branch: bamloader
Log Message:
Improved bam_flag udfs by using lookup tables instead of serial string
comparison
diffs (96 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
@@ -26,26 +26,78 @@
#include "monetdb_config.h"
#include "bam_lib.h"
-#define flag_str2sht(flag_str) \
- (strcmp(flag_str, "mult_segm") == 0 ? 0 : \
- (strcmp(flag_str, "prop_alig") == 0 ? 1 : \
- (strcmp(flag_str, "segm_unma") == 0 ? 2 : \
- (strcmp(flag_str, "next_unma") == 0 ? 3 : \
- (strcmp(flag_str, "segm_reve") == 0 ? 4 :
\
- (strcmp(flag_str, "next_reve") == 0 ? 5 :
\
- (strcmp(flag_str, "firs_segm") == 0 ? 6 :
\
- (strcmp(flag_str, "last_segm") == 0 ? 7 : \
- (strcmp(flag_str, "seco_alig") == 0 ? 8 : \
- (strcmp(flag_str, "qual_cont") == 0 ? 9 : \
- (strcmp(flag_str, "opti_dupl") == 0 ? 10 : \
- (strcmp(flag_str, "supp_alig") == 0 ? 11 : -1))))))))))))
+/* Map string to integer by adding all odd and subtracting all even numbers
+ * For the strings that we want to detect, this gives the following:
+ * mult_segm -> 71
+ * prop_alig -> 101
+ * segm_unma -> 84
+ * next_unma -> 89
+ * segm_reve -> 73
+ * next_reve -> 78
+ * firs_segm -> 83
+ * last_segm -> 97
+ * seco_alig -> 106
+ * qual_cont -> 98
+ * opti_dupl -> 118
+ * supp_alig -> 102
+ *
+ * These integers fit in an array of 48 positions
+ * Define two arrays:
+ * - One that maps int position to the bit position that we
+ * are looking for
+ * - One that maps bit position to string, so we can check if
+ * the input really was one of the valid strings (since many)
+ * strings will map to the same integer
+ */
+
+sht intbit_map[] = {
+ 0, -1, 4, -1, -1, -1, -1, 5, -1, -1,
+ -1, -1, 6, 2, -1, -1, -1, -1, 3, -1,
+ -1, -1, -1, -1, -1, -1, 7, 9, -1, -1,
+ 1, 11, -1, -1, -1, 8, -1, -1, -1, -1,
+ -1, -1, -1, -1, -1, -1, -1, 10
+};
+
+str posstr_map[] = {
+ "mult_segm",
+ "prop_alig",
+ "segm_unma",
+ "next_unma",
+ "segm_reve",
+ "next_reve",
+ "firs_segm",
+ "last_segm",
+ "seco_alig",
+ "qual_cont",
+ "opti_dupl",
+ "supp_alig"
+};
+
+static sht
+flag_str2sht(str flag_str) {
+ int i = 0;
+ int mult = 1;
+ int strnum = -71;
+ char c;
+ sht k = -1;
+ while((c = flag_str[i++]) != '\0') {
+ strnum += mult * (int)c;
+ mult *= -1;
+ }
+ if(strnum < 0 || strnum > 47 || (k = intbit_map[strnum]) < 0 ||
+ strcmp(posstr_map[k], flag_str) != 0) {
+ k = -1;
+ }
+ return k;
+}
#define kth_bit(flag, k) ((flag & (1 << k)) == (1 << k))
str
bam_flag(bit * ret, sht * flag, str * name)
{
- sht k = flag_str2sht(*name);
+ sht k;
+ k = flag_str2sht(*name);
if (k < 0)
throw(MAL, "bam_flag", "Unknown flag name given: %s\n",
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