| /dports/biology/py-pysam/pysam-0.18.0/samtools/ |
| H A D | bam2depth.c | 80 int remove_overlaps; member
515 if (opt->remove_overlaps) { in fastdepth_core()
746 .remove_overlaps = 0, in main_depth()
824 opt.remove_overlaps = 1; in main_depth()
893 | (opt.remove_overlaps ? SAM_QNAME|SAM_RNEXT|SAM_PNEXT in main_depth()
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| H A D | bam2depth.c.pysam.c | 82 int remove_overlaps; member
517 if (opt->remove_overlaps) { in fastdepth_core()
748 .remove_overlaps = 0, in main_depth()
826 opt.remove_overlaps = 1; in main_depth()
895 | (opt.remove_overlaps ? SAM_QNAME|SAM_RNEXT|SAM_PNEXT in main_depth()
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| H A D | stats.c | 160 int remove_overlaps; member
1019 static void remove_overlaps(bam1_t *bam_line, khash_t(qn2pair) *read_pairs, stats_t *stats, hts_pos… in remove_overlaps() function
1385 if ( stats->info->remove_overlaps ) in collect_stats()
1386 remove_overlaps(bam_line, read_pairs, stats, pmin, pmax); in collect_stats()
1415 if ( stats->info->remove_overlaps ) in collect_stats()
1416 remove_overlaps(bam_line, read_pairs, stats, p, p+oplen); in collect_stats()
1426 if ( stats->info->remove_overlaps ) in collect_stats()
1427 … remove_overlaps(bam_line, read_pairs, stats, -1LL, -1LL); //remove the line from the hash table in collect_stats()
2194 info->remove_overlaps = 0; in stats_info_init()
2431 case 'p': info->remove_overlaps = 1; break; in main_stats()
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| H A D | stats.c.pysam.c | 162 int remove_overlaps; member
1021 static void remove_overlaps(bam1_t *bam_line, khash_t(qn2pair) *read_pairs, stats_t *stats, hts_pos… in remove_overlaps() function
1387 if ( stats->info->remove_overlaps ) in collect_stats()
1388 remove_overlaps(bam_line, read_pairs, stats, pmin, pmax); in collect_stats()
1417 if ( stats->info->remove_overlaps ) in collect_stats()
1418 remove_overlaps(bam_line, read_pairs, stats, p, p+oplen); in collect_stats()
1428 if ( stats->info->remove_overlaps ) in collect_stats()
1429 … remove_overlaps(bam_line, read_pairs, stats, -1LL, -1LL); //remove the line from the hash table in collect_stats()
2196 info->remove_overlaps = 0; in stats_info_init()
2433 case 'p': info->remove_overlaps = 1; break; in main_stats()
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| /dports/biology/samtools/samtools-1.14/ |
| H A D | bam2depth.c | 80 int remove_overlaps; member
515 if (opt->remove_overlaps) { in fastdepth_core()
746 .remove_overlaps = 0, in main_depth()
824 opt.remove_overlaps = 1; in main_depth()
893 | (opt.remove_overlaps ? SAM_QNAME|SAM_RNEXT|SAM_PNEXT in main_depth()
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| H A D | stats.c | 160 int remove_overlaps; member
1019 static void remove_overlaps(bam1_t *bam_line, khash_t(qn2pair) *read_pairs, stats_t *stats, hts_pos… in remove_overlaps() function
1385 if ( stats->info->remove_overlaps ) in collect_stats()
1386 remove_overlaps(bam_line, read_pairs, stats, pmin, pmax); in collect_stats()
1415 if ( stats->info->remove_overlaps ) in collect_stats()
1416 remove_overlaps(bam_line, read_pairs, stats, p, p+oplen); in collect_stats()
1426 if ( stats->info->remove_overlaps ) in collect_stats()
1427 … remove_overlaps(bam_line, read_pairs, stats, -1LL, -1LL); //remove the line from the hash table in collect_stats()
2194 info->remove_overlaps = 0; in stats_info_init()
2431 case 'p': info->remove_overlaps = 1; break; in main_stats()
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| /dports/www/elinks/elinks-0.11.7/src/cache/ |
| H A D | cache.c | 324 remove_overlaps(struct cache_entry *cached, struct fragment *f, int *trunc) in remove_overlaps() function
428 remove_overlaps(cached, f, &trunc); in add_fragment()
461 remove_overlaps(cached, nf, &trunc); in add_fragment()
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| /dports/biology/freebayes/freebayes-1.3.5/contrib/SeqLib/SeqLib/ |
| H A D | aho_corasick.hpp | 198 interval_collection remove_overlaps(const interval_collection& intervals) { in remove_overlaps() function in aho_corasick::interval_tree
435 basic_trie& remove_overlaps() { in remove_overlaps() function in aho_corasick::basic_trie
497 auto tmp = tree.remove_overlaps(collected_ahoemits); in parse_text()
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| /dports/x11-fonts/py-fontmake/fontmake-1.8.0/Lib/fontmake/ |
| H A D | font_project.py | 171 def remove_overlaps(self, ufos, glyph_filter=lambda g: len(g)): member in FontProject
305 remove_overlaps=True, argument
417 removeOverlaps=remove_overlaps,
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| /dports/security/libfprint/libfprint-0.7.0/libfprint/nbis/mindtct/ |
| H A D | remove.c | 1143 static int remove_overlaps(MINUTIAE *minutiae, in remove_overlaps() function
2242 if((ret = remove_overlaps(minutiae, bdata, iw, ih, lfsparms))){ in remove_false_minutia_V2()
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| /dports/print/py-fonttools/fonttools-4.28.2/Lib/fontTools/varLib/instancer/ |
| H A D | __init__.py | 1384 if options.remove_overlaps:
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| /dports/biology/gmap/gmap-2020-09-12/ |
| H A D | ChangeLog | 12948 * stage3hr.c: Restored usage of score before nmatches in remove_overlaps
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