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@ -25,6 +25,7 @@ |
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#define XDL_KPDIS_RUN 4 |
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#define XDL_KPDIS_RUN 4 |
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#define XDL_MAX_EQLIMIT 1024 |
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@ -305,26 +306,48 @@ void xdl_free_env(xdfenv_t *xe) { |
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static int xdl_clean_mmatch(char const *dis, long i, long s, long e) { |
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static int xdl_clean_mmatch(char const *dis, long i, long s, long e) { |
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long r, rdis, rpdis; |
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long r, rdis0, rpdis0, rdis1, rpdis1; |
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for (r = 1, rdis = 0, rpdis = 1; (i - r) >= s; r++) { |
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/* |
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* Scans the lines before 'i' to find a run of lines that either |
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* have no match (dis[j] == 0) or have multiple matches (dis[j] > 1). |
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* Note that we always call this function with dis[i] > 1, so the |
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* current line (i) is already a multimatch line. |
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*/ |
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for (r = 1, rdis0 = 0, rpdis0 = 1; (i - r) >= s; r++) { |
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if (!dis[i - r]) |
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if (!dis[i - r]) |
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rdis++; |
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rdis0++; |
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else if (dis[i - r] == 2) |
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else if (dis[i - r] == 2) |
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rpdis++; |
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rpdis0++; |
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else |
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else |
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break; |
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break; |
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} |
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} |
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for (r = 1; (i + r) <= e; r++) { |
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/* |
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* If the run before the line 'i' found only multimatch lines, we |
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* return 0 and hence we don't make the current line (i) discarded. |
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* We want to discard multimatch lines only when they appear in the |
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* middle of runs with nomatch lines (dis[j] == 0). |
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*/ |
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if (rdis0 == 0) |
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return 0; |
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for (r = 1, rdis1 = 0, rpdis1 = 1; (i + r) <= e; r++) { |
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if (!dis[i + r]) |
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if (!dis[i + r]) |
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rdis++; |
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rdis1++; |
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else if (dis[i + r] == 2) |
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else if (dis[i + r] == 2) |
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rpdis++; |
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rpdis1++; |
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else |
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else |
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break; |
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break; |
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} |
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} |
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/* |
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return rpdis * XDL_KPDIS_RUN < (rpdis + rdis); |
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* If the run after the line 'i' found only multimatch lines, we |
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* return 0 and hence we don't make the current line (i) discarded. |
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*/ |
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if (rdis1 == 0) |
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return 0; |
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rdis1 += rdis0; |
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rpdis1 += rpdis0; |
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return rpdis1 * XDL_KPDIS_RUN < (rpdis1 + rdis1); |
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} |
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} |
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@ -334,34 +357,40 @@ static int xdl_clean_mmatch(char const *dis, long i, long s, long e) { |
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* might be potentially discarded if they happear in a run of discardable. |
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* might be potentially discarded if they happear in a run of discardable. |
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*/ |
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*/ |
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static int xdl_cleanup_records(xdfile_t *xdf1, xdfile_t *xdf2) { |
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static int xdl_cleanup_records(xdfile_t *xdf1, xdfile_t *xdf2) { |
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long i, rhi, nreff; |
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long i, nm, rhi, nreff, mlim; |
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unsigned long hav; |
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unsigned long hav; |
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xrecord_t **recs; |
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xrecord_t **recs; |
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xrecord_t *rec; |
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xrecord_t *rec; |
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char *dis, *dis1, *dis2; |
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char *dis, *dis1, *dis2; |
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if (!(dis = (char *) xdl_malloc((xdf1->nrec + xdf2->nrec + 2) * sizeof(char)))) { |
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if (!(dis = (char *) xdl_malloc(xdf1->nrec + xdf2->nrec + 2))) { |
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return -1; |
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return -1; |
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} |
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} |
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memset(dis, 0, (xdf1->nrec + xdf2->nrec + 2) * sizeof(char)); |
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memset(dis, 0, xdf1->nrec + xdf2->nrec + 2); |
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dis1 = dis; |
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dis1 = dis; |
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dis2 = dis1 + xdf1->nrec + 1; |
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dis2 = dis1 + xdf1->nrec + 1; |
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if ((mlim = xdl_bogosqrt(xdf1->nrec)) > XDL_MAX_EQLIMIT) |
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mlim = XDL_MAX_EQLIMIT; |
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for (i = xdf1->dstart, recs = &xdf1->recs[xdf1->dstart]; i <= xdf1->dend; i++, recs++) { |
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for (i = xdf1->dstart, recs = &xdf1->recs[xdf1->dstart]; i <= xdf1->dend; i++, recs++) { |
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hav = (*recs)->ha; |
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hav = (*recs)->ha; |
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rhi = (long) XDL_HASHLONG(hav, xdf2->hbits); |
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rhi = (long) XDL_HASHLONG(hav, xdf2->hbits); |
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for (rec = xdf2->rhash[rhi]; rec; rec = rec->next) |
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for (nm = 0, rec = xdf2->rhash[rhi]; rec; rec = rec->next) |
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if (rec->ha == hav && ++dis1[i] == 2) |
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if (rec->ha == hav && ++nm == mlim) |
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break; |
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break; |
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dis1[i] = (nm == 0) ? 0: (nm >= mlim) ? 2: 1; |
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} |
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} |
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if ((mlim = xdl_bogosqrt(xdf2->nrec)) > XDL_MAX_EQLIMIT) |
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mlim = XDL_MAX_EQLIMIT; |
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for (i = xdf2->dstart, recs = &xdf2->recs[xdf2->dstart]; i <= xdf2->dend; i++, recs++) { |
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for (i = xdf2->dstart, recs = &xdf2->recs[xdf2->dstart]; i <= xdf2->dend; i++, recs++) { |
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hav = (*recs)->ha; |
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hav = (*recs)->ha; |
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rhi = (long) XDL_HASHLONG(hav, xdf1->hbits); |
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rhi = (long) XDL_HASHLONG(hav, xdf1->hbits); |
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for (rec = xdf1->rhash[rhi]; rec; rec = rec->next) |
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for (nm = 0, rec = xdf1->rhash[rhi]; rec; rec = rec->next) |
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if (rec->ha == hav && ++dis2[i] == 2) |
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if (rec->ha == hav && ++nm == mlim) |
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break; |
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break; |
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dis2[i] = (nm == 0) ? 0: (nm >= mlim) ? 2: 1; |
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} |
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} |
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for (nreff = 0, i = xdf1->dstart, recs = &xdf1->recs[xdf1->dstart]; |
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for (nreff = 0, i = xdf1->dstart, recs = &xdf1->recs[xdf1->dstart]; |
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