#define XDL_KPDIS_RUN 4
+#define XDL_MAX_EQLIMIT 1024
static int xdl_clean_mmatch(char const *dis, long i, long s, long e) {
- long r, rdis, rpdis;
-
- for (r = 1, rdis = 0, rpdis = 1; (i - r) >= s; r++) {
+ long r, rdis0, rpdis0, rdis1, rpdis1;
+
+ /*
+ * Scans the lines before 'i' to find a run of lines that either
+ * have no match (dis[j] == 0) or have multiple matches (dis[j] > 1).
+ * Note that we always call this function with dis[i] > 1, so the
+ * current line (i) is already a multimatch line.
+ */
+ for (r = 1, rdis0 = 0, rpdis0 = 1; (i - r) >= s; r++) {
if (!dis[i - r])
- rdis++;
+ rdis0++;
else if (dis[i - r] == 2)
- rpdis++;
+ rpdis0++;
else
break;
}
- for (r = 1; (i + r) <= e; r++) {
+ /*
+ * If the run before the line 'i' found only multimatch lines, we
+ * return 0 and hence we don't make the current line (i) discarded.
+ * We want to discard multimatch lines only when they appear in the
+ * middle of runs with nomatch lines (dis[j] == 0).
+ */
+ if (rdis0 == 0)
+ return 0;
+ for (r = 1, rdis1 = 0, rpdis1 = 1; (i + r) <= e; r++) {
if (!dis[i + r])
- rdis++;
+ rdis1++;
else if (dis[i + r] == 2)
- rpdis++;
+ rpdis1++;
else
break;
}
-
- return rpdis * XDL_KPDIS_RUN < (rpdis + rdis);
+ /*
+ * If the run after the line 'i' found only multimatch lines, we
+ * return 0 and hence we don't make the current line (i) discarded.
+ */
+ if (rdis1 == 0)
+ return 0;
+ rdis1 += rdis0;
+ rpdis1 += rpdis0;
+
+ return rpdis1 * XDL_KPDIS_RUN < (rpdis1 + rdis1);
}
* might be potentially discarded if they happear in a run of discardable.
*/
static int xdl_cleanup_records(xdfile_t *xdf1, xdfile_t *xdf2) {
- long i, rhi, nreff;
+ long i, nm, rhi, nreff, mlim;
unsigned long hav;
xrecord_t **recs;
xrecord_t *rec;
char *dis, *dis1, *dis2;
- if (!(dis = (char *) xdl_malloc((xdf1->nrec + xdf2->nrec + 2) * sizeof(char)))) {
+ if (!(dis = (char *) xdl_malloc(xdf1->nrec + xdf2->nrec + 2))) {
return -1;
}
- memset(dis, 0, (xdf1->nrec + xdf2->nrec + 2) * sizeof(char));
+ memset(dis, 0, xdf1->nrec + xdf2->nrec + 2);
dis1 = dis;
dis2 = dis1 + xdf1->nrec + 1;
+ if ((mlim = xdl_bogosqrt(xdf1->nrec)) > XDL_MAX_EQLIMIT)
+ mlim = XDL_MAX_EQLIMIT;
for (i = xdf1->dstart, recs = &xdf1->recs[xdf1->dstart]; i <= xdf1->dend; i++, recs++) {
hav = (*recs)->ha;
rhi = (long) XDL_HASHLONG(hav, xdf2->hbits);
- for (rec = xdf2->rhash[rhi]; rec; rec = rec->next)
- if (rec->ha == hav && ++dis1[i] == 2)
+ for (nm = 0, rec = xdf2->rhash[rhi]; rec; rec = rec->next)
+ if (rec->ha == hav && ++nm == mlim)
break;
+ dis1[i] = (nm == 0) ? 0: (nm >= mlim) ? 2: 1;
}
+ if ((mlim = xdl_bogosqrt(xdf2->nrec)) > XDL_MAX_EQLIMIT)
+ mlim = XDL_MAX_EQLIMIT;
for (i = xdf2->dstart, recs = &xdf2->recs[xdf2->dstart]; i <= xdf2->dend; i++, recs++) {
hav = (*recs)->ha;
rhi = (long) XDL_HASHLONG(hav, xdf1->hbits);
- for (rec = xdf1->rhash[rhi]; rec; rec = rec->next)
- if (rec->ha == hav && ++dis2[i] == 2)
+ for (nm = 0, rec = xdf1->rhash[rhi]; rec; rec = rec->next)
+ if (rec->ha == hav && ++nm == mlim)
break;
+ dis2[i] = (nm == 0) ? 0: (nm >= mlim) ? 2: 1;
}
for (nreff = 0, i = xdf1->dstart, recs = &xdf1->recs[xdf1->dstart];
+long xdl_bogosqrt(long n) {
+ long i;
+
+ /*
+ * Classical integer square root approximation using shifts.
+ */
+ for (i = 1; n > 0; n >>= 2)
+ i <<= 1;
+
+ return i;
+}
+
+
int xdl_emit_diffrec(char const *rec, long size, char const *pre, long psize,
xdemitcb_t *ecb) {
mmbuffer_t mb[3];
memcpy(buf, "@@ -", 4);
nb += 4;
- nb += xdl_num_out(buf + nb, c1 ? s1: 0);
+ nb += xdl_num_out(buf + nb, c1 ? s1: s1 - 1);
if (c1 != 1) {
memcpy(buf + nb, ",", 1);
memcpy(buf + nb, " +", 2);
nb += 2;
- nb += xdl_num_out(buf + nb, c2 ? s2: 0);
+ nb += xdl_num_out(buf + nb, c2 ? s2: s2 - 1);
if (c2 != 1) {
memcpy(buf + nb, ",", 1);