| /dports/biology/py-pysam/pysam-0.18.0/htslib/htslib/ |
| H A D | synced_bcf_reader.h | 140 typedef struct bcf_sr_t struct
153 bcf_sr_t; argument
177 bcf_sr_t *readers;
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| /dports/biology/freebayes/freebayes-1.3.5/contrib/htslib/htslib/ |
| H A D | synced_bcf_reader.h | 137 typedef struct bcf_sr_t struct
150 bcf_sr_t; argument
174 bcf_sr_t *readers;
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| /dports/biology/htslib/htslib-1.14/htslib/ |
| H A D | synced_bcf_reader.h | 140 typedef struct bcf_sr_t struct
153 bcf_sr_t; argument
177 bcf_sr_t *readers;
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| /dports/biology/vt/vt-0.57721/lib/htslib/ |
| H A D | synced_bcf_reader.c | 210 files->readers = (bcf_sr_t*) realloc(files->readers, sizeof(bcf_sr_t)*(files->nreaders+1)); in bcf_sr_add_reader()
211 bcf_sr_t *reader = &files->readers[files->nreaders++]; in bcf_sr_add_reader()
212 memset(reader,0,sizeof(bcf_sr_t)); in bcf_sr_add_reader()
332 static void bcf_sr_destroy1(bcf_sr_t *reader) in bcf_sr_destroy1()
373 memmove(&files->readers[i], &files->readers[i+1], (files->nreaders-i-1)*sizeof(bcf_sr_t)); in bcf_sr_remove_reader()
380 void debug_buffer(FILE *fp, bcf_sr_t *reader) in debug_buffer()
404 static inline int has_filter(bcf_sr_t *reader, bcf1_t *line) in has_filter()
421 static int _reader_seek(bcf_sr_t *reader, const char *seq, int start, int end) in _reader_seek()
482 static void _reader_fill_buffer(bcf_srs_t *files, bcf_sr_t *reader) in _reader_fill_buffer()
563 static void _reader_shift_buffer(bcf_sr_t *reader) in _reader_shift_buffer()
[all …]
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| /dports/biology/bedtools/bedtools2-2.30.0/src/utils/htslib/ |
| H A D | synced_bcf_reader.c | 210 files->readers = (bcf_sr_t*) realloc(files->readers, sizeof(bcf_sr_t)*(files->nreaders+1)); in bcf_sr_add_reader()
211 bcf_sr_t *reader = &files->readers[files->nreaders++]; in bcf_sr_add_reader()
212 memset(reader,0,sizeof(bcf_sr_t)); in bcf_sr_add_reader()
332 static void bcf_sr_destroy1(bcf_sr_t *reader) in bcf_sr_destroy1()
373 memmove(&files->readers[i], &files->readers[i+1], (files->nreaders-i-1)*sizeof(bcf_sr_t)); in bcf_sr_remove_reader()
380 void debug_buffer(FILE *fp, bcf_sr_t *reader) in debug_buffer()
404 static inline int has_filter(bcf_sr_t *reader, bcf1_t *line) in has_filter()
421 static int _reader_seek(bcf_sr_t *reader, const char *seq, int start, int end) in _reader_seek()
482 static void _reader_fill_buffer(bcf_srs_t *files, bcf_sr_t *reader) in _reader_fill_buffer()
563 static void _reader_shift_buffer(bcf_sr_t *reader) in _reader_shift_buffer()
[all …]
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| /dports/biology/stacks/stacks-2.4/htslib/ |
| H A D | synced_bcf_reader.c | 210 files->readers = (bcf_sr_t*) realloc(files->readers, sizeof(bcf_sr_t)*(files->nreaders+1)); in bcf_sr_add_reader()
211 bcf_sr_t *reader = &files->readers[files->nreaders++]; in bcf_sr_add_reader()
212 memset(reader,0,sizeof(bcf_sr_t)); in bcf_sr_add_reader()
332 static void bcf_sr_destroy1(bcf_sr_t *reader) in bcf_sr_destroy1()
373 memmove(&files->readers[i], &files->readers[i+1], (files->nreaders-i-1)*sizeof(bcf_sr_t)); in bcf_sr_remove_reader()
380 void debug_buffer(FILE *fp, bcf_sr_t *reader) in debug_buffer()
404 static inline int has_filter(bcf_sr_t *reader, bcf1_t *line) in has_filter()
421 static int _reader_seek(bcf_sr_t *reader, const char *seq, int start, int end) in _reader_seek()
482 static void _reader_fill_buffer(bcf_srs_t *files, bcf_sr_t *reader) in _reader_fill_buffer()
563 static void _reader_shift_buffer(bcf_sr_t *reader) in _reader_shift_buffer()
[all …]
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| /dports/biology/kallisto/kallisto-0.46.1/ext/htslib/ |
| H A D | synced_bcf_reader.c | 210 files->readers = (bcf_sr_t*) realloc(files->readers, sizeof(bcf_sr_t)*(files->nreaders+1)); in bcf_sr_add_reader()
211 bcf_sr_t *reader = &files->readers[files->nreaders++]; in bcf_sr_add_reader()
212 memset(reader,0,sizeof(bcf_sr_t)); in bcf_sr_add_reader()
332 static void bcf_sr_destroy1(bcf_sr_t *reader) in bcf_sr_destroy1()
373 memmove(&files->readers[i], &files->readers[i+1], (files->nreaders-i-1)*sizeof(bcf_sr_t)); in bcf_sr_remove_reader()
380 void debug_buffer(FILE *fp, bcf_sr_t *reader) in debug_buffer()
404 static inline int has_filter(bcf_sr_t *reader, bcf1_t *line) in has_filter()
421 static int _reader_seek(bcf_sr_t *reader, const char *seq, int start, int end) in _reader_seek()
480 static void _reader_fill_buffer(bcf_srs_t *files, bcf_sr_t *reader) in _reader_fill_buffer()
561 static void _reader_shift_buffer(bcf_sr_t *reader) in _reader_shift_buffer()
[all …]
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| H A D | bcf_sr_sort.c | 358 bcf_sr_t *reader = &readers->readers[ireader]; in bcf_sr_sort_set()
545 bcf_sr_t *reader = &readers->readers[0]; in bcf_sr_sort_next()
579 bcf_sr_t *reader = &srt->sr->readers[i]; in bcf_sr_sort_next()
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| /dports/biology/freebayes/freebayes-1.3.5/contrib/htslib/ |
| H A D | synced_bcf_reader.c | 238 files->readers = (bcf_sr_t*) realloc(files->readers, sizeof(bcf_sr_t)*(files->nreaders+1)); in bcf_sr_add_reader()
239 bcf_sr_t *reader = &files->readers[files->nreaders++]; in bcf_sr_add_reader()
240 memset(reader,0,sizeof(bcf_sr_t)); in bcf_sr_add_reader()
392 static void bcf_sr_destroy1(bcf_sr_t *reader) in bcf_sr_destroy1()
433 memmove(&files->readers[i], &files->readers[i+1], (files->nreaders-i-1)*sizeof(bcf_sr_t)); in bcf_sr_remove_reader()
440 void debug_buffer(FILE *fp, bcf_sr_t *reader) in debug_buffer()
465 static inline int has_filter(bcf_sr_t *reader, bcf1_t *line) in has_filter()
482 static int _reader_seek(bcf_sr_t *reader, const char *seq, hts_pos_t start, hts_pos_t end) in _reader_seek()
546 static int _reader_fill_buffer(bcf_srs_t *files, bcf_sr_t *reader) in _reader_fill_buffer()
637 static void _reader_shift_buffer(bcf_sr_t *reader) in _reader_shift_buffer()
[all …]
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| /dports/biology/vt/vt-0.57721/lib/htslib/htslib/ |
| H A D | synced_bcf_reader.h | 146 bcf_sr_t; typedef
170 bcf_sr_t *readers;
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| /dports/biology/bedtools/bedtools2-2.30.0/src/utils/htslib/htslib/ |
| H A D | synced_bcf_reader.h | 146 bcf_sr_t; typedef
170 bcf_sr_t *readers;
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| /dports/biology/stacks/stacks-2.4/htslib/htslib/ |
| H A D | synced_bcf_reader.h | 146 bcf_sr_t; typedef
170 bcf_sr_t *readers;
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| /dports/biology/kallisto/kallisto-0.46.1/ext/htslib/htslib/ |
| H A D | synced_bcf_reader.h | 146 bcf_sr_t; typedef
170 bcf_sr_t *readers;
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| /dports/biology/py-pysam/pysam-0.18.0/htslib/ |
| H A D | synced_bcf_reader.c | 258 files->readers = (bcf_sr_t*) realloc(files->readers, sizeof(bcf_sr_t)*(files->nreaders+1)); in bcf_sr_add_reader()
259 bcf_sr_t *reader = &files->readers[files->nreaders++]; in bcf_sr_add_reader()
260 memset(reader,0,sizeof(bcf_sr_t)); in bcf_sr_add_reader()
414 static void bcf_sr_destroy1(bcf_sr_t *reader) in bcf_sr_destroy1()
455 memmove(&files->readers[i], &files->readers[i+1], (files->nreaders-i-1)*sizeof(bcf_sr_t)); in bcf_sr_remove_reader()
462 void debug_buffer(FILE *fp, bcf_sr_t *reader) in debug_buffer()
487 static inline int has_filter(bcf_sr_t *reader, bcf1_t *line) in has_filter()
504 static int _reader_seek(bcf_sr_t *reader, const char *seq, hts_pos_t start, hts_pos_t end) in _reader_seek()
597 static int _reader_fill_buffer(bcf_srs_t *files, bcf_sr_t *reader) in _reader_fill_buffer()
708 static void _reader_shift_buffer(bcf_sr_t *reader) in _reader_shift_buffer()
[all …]
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| /dports/biology/htslib/htslib-1.14/ |
| H A D | synced_bcf_reader.c | 258 files->readers = (bcf_sr_t*) realloc(files->readers, sizeof(bcf_sr_t)*(files->nreaders+1)); in bcf_sr_add_reader()
259 bcf_sr_t *reader = &files->readers[files->nreaders++]; in bcf_sr_add_reader()
260 memset(reader,0,sizeof(bcf_sr_t)); in bcf_sr_add_reader()
414 static void bcf_sr_destroy1(bcf_sr_t *reader) in bcf_sr_destroy1()
455 memmove(&files->readers[i], &files->readers[i+1], (files->nreaders-i-1)*sizeof(bcf_sr_t)); in bcf_sr_remove_reader()
462 void debug_buffer(FILE *fp, bcf_sr_t *reader) in debug_buffer()
487 static inline int has_filter(bcf_sr_t *reader, bcf1_t *line) in has_filter()
504 static int _reader_seek(bcf_sr_t *reader, const char *seq, hts_pos_t start, hts_pos_t end) in _reader_seek()
597 static int _reader_fill_buffer(bcf_srs_t *files, bcf_sr_t *reader) in _reader_fill_buffer()
708 static void _reader_shift_buffer(bcf_sr_t *reader) in _reader_shift_buffer()
[all …]
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| /dports/biology/bcftools/bcftools-1.14/ |
| H A D | vcfstats.c | 618 static void init_iaf(args_t *args, bcf_sr_t *reader) in init_iaf()
676 static inline void do_mnp_stats(args_t *args, stats_t *stats, bcf_sr_t *reader) in do_mnp_stats()
681 static inline void do_other_stats(args_t *args, stats_t *stats, bcf_sr_t *reader) in do_other_stats()
686 static void do_indel_stats(args_t *args, stats_t *stats, bcf_sr_t *reader) in do_indel_stats()
793 static void do_user_stats(stats_t *stats, bcf_sr_t *reader, int is_ts) in do_user_stats()
821 static void do_snp_stats(args_t *args, stats_t *stats, bcf_sr_t *reader) in do_snp_stats()
898 static void do_sample_stats(args_t *args, stats_t *stats, bcf_sr_t *reader, int matched) in do_sample_stats()
1129 bcf_sr_t *reader = &files->readers[0]; in do_sample_stats()
1150 bcf_sr_t *reader = NULL; in do_vcf_stats()
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| H A D | vcfmerge.c | 902 bcf_sr_t *reader = &files->readers[i]; in merge_chrom2qual()
1013 bcf_sr_t *reader = &files->readers[i]; in merge_filter()
1263 bcf_sr_t *reader = &files->readers[i]; in merge_info()
1416 bcf_sr_t *reader = &files->readers[i]; in init_local_alleles()
1535 bcf_sr_t *reader = &files->readers[i]; in update_local_alleles()
1596 bcf_sr_t *reader = &files->readers[i]; in merge_GT()
1703 bcf_sr_t *reader = &files->readers[i]; in merge_format_string()
1807 bcf_sr_t *reader = &files->readers[i]; in merge_localized_numberG_format_field()
1908 bcf_sr_t *reader = &files->readers[i]; in merge_localized_numberAR_format_field()
2046 bcf_sr_t *reader = &files->readers[i]; in merge_format_field()
[all …]
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| /dports/biology/bio-mocha/bcftools-1.14/ |
| H A D | vcfstats.c | 618 static void init_iaf(args_t *args, bcf_sr_t *reader) in init_iaf()
676 static inline void do_mnp_stats(args_t *args, stats_t *stats, bcf_sr_t *reader) in do_mnp_stats()
681 static inline void do_other_stats(args_t *args, stats_t *stats, bcf_sr_t *reader) in do_other_stats()
686 static void do_indel_stats(args_t *args, stats_t *stats, bcf_sr_t *reader) in do_indel_stats()
793 static void do_user_stats(stats_t *stats, bcf_sr_t *reader, int is_ts) in do_user_stats()
821 static void do_snp_stats(args_t *args, stats_t *stats, bcf_sr_t *reader) in do_snp_stats()
898 static void do_sample_stats(args_t *args, stats_t *stats, bcf_sr_t *reader, int matched) in do_sample_stats()
1129 bcf_sr_t *reader = &files->readers[0]; in do_sample_stats()
1150 bcf_sr_t *reader = NULL; in do_vcf_stats()
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| H A D | vcfmerge.c | 902 bcf_sr_t *reader = &files->readers[i]; in merge_chrom2qual()
1013 bcf_sr_t *reader = &files->readers[i]; in merge_filter()
1263 bcf_sr_t *reader = &files->readers[i]; in merge_info()
1416 bcf_sr_t *reader = &files->readers[i]; in init_local_alleles()
1535 bcf_sr_t *reader = &files->readers[i]; in update_local_alleles()
1596 bcf_sr_t *reader = &files->readers[i]; in merge_GT()
1703 bcf_sr_t *reader = &files->readers[i]; in merge_format_string()
1807 bcf_sr_t *reader = &files->readers[i]; in merge_localized_numberG_format_field()
1908 bcf_sr_t *reader = &files->readers[i]; in merge_localized_numberAR_format_field()
2046 bcf_sr_t *reader = &files->readers[i]; in merge_format_field()
[all …]
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| /dports/biology/py-pysam/pysam-0.18.0/bcftools/ |
| H A D | vcfstats.c | 618 static void init_iaf(args_t *args, bcf_sr_t *reader) in init_iaf()
676 static inline void do_mnp_stats(args_t *args, stats_t *stats, bcf_sr_t *reader) in do_mnp_stats()
681 static inline void do_other_stats(args_t *args, stats_t *stats, bcf_sr_t *reader) in do_other_stats()
686 static void do_indel_stats(args_t *args, stats_t *stats, bcf_sr_t *reader) in do_indel_stats()
793 static void do_user_stats(stats_t *stats, bcf_sr_t *reader, int is_ts) in do_user_stats()
821 static void do_snp_stats(args_t *args, stats_t *stats, bcf_sr_t *reader) in do_snp_stats()
898 static void do_sample_stats(args_t *args, stats_t *stats, bcf_sr_t *reader, int matched) in do_sample_stats()
1129 bcf_sr_t *reader = &files->readers[0]; in do_sample_stats()
1150 bcf_sr_t *reader = NULL; in do_vcf_stats()
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| H A D | vcfmerge.c | 902 bcf_sr_t *reader = &files->readers[i]; in merge_chrom2qual()
1013 bcf_sr_t *reader = &files->readers[i]; in merge_filter()
1263 bcf_sr_t *reader = &files->readers[i]; in merge_info()
1416 bcf_sr_t *reader = &files->readers[i]; in init_local_alleles()
1535 bcf_sr_t *reader = &files->readers[i]; in update_local_alleles()
1596 bcf_sr_t *reader = &files->readers[i]; in merge_GT()
1703 bcf_sr_t *reader = &files->readers[i]; in merge_format_string()
1807 bcf_sr_t *reader = &files->readers[i]; in merge_localized_numberG_format_field()
1908 bcf_sr_t *reader = &files->readers[i]; in merge_localized_numberAR_format_field()
2046 bcf_sr_t *reader = &files->readers[i]; in merge_format_field()
[all …]
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| H A D | vcfmerge.c.pysam.c | 904 bcf_sr_t *reader = &files->readers[i]; in merge_chrom2qual()
1015 bcf_sr_t *reader = &files->readers[i]; in merge_filter()
1265 bcf_sr_t *reader = &files->readers[i]; in merge_info()
1418 bcf_sr_t *reader = &files->readers[i]; in init_local_alleles()
1537 bcf_sr_t *reader = &files->readers[i]; in update_local_alleles()
1598 bcf_sr_t *reader = &files->readers[i]; in merge_GT()
1705 bcf_sr_t *reader = &files->readers[i]; in merge_format_string()
1809 bcf_sr_t *reader = &files->readers[i]; in merge_localized_numberG_format_field()
1910 bcf_sr_t *reader = &files->readers[i]; in merge_localized_numberAR_format_field()
2048 bcf_sr_t *reader = &files->readers[i]; in merge_format_field()
[all …]
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| H A D | vcfstats.c.pysam.c | 620 static void init_iaf(args_t *args, bcf_sr_t *reader) in init_iaf()
678 static inline void do_mnp_stats(args_t *args, stats_t *stats, bcf_sr_t *reader) in do_mnp_stats()
683 static inline void do_other_stats(args_t *args, stats_t *stats, bcf_sr_t *reader) in do_other_stats()
688 static void do_indel_stats(args_t *args, stats_t *stats, bcf_sr_t *reader) in do_indel_stats()
795 static void do_user_stats(stats_t *stats, bcf_sr_t *reader, int is_ts) in do_user_stats()
823 static void do_snp_stats(args_t *args, stats_t *stats, bcf_sr_t *reader) in do_snp_stats()
900 static void do_sample_stats(args_t *args, stats_t *stats, bcf_sr_t *reader, int matched) in do_sample_stats()
1131 bcf_sr_t *reader = &files->readers[0]; in do_sample_stats()
1152 bcf_sr_t *reader = NULL; in do_vcf_stats()
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| /dports/biology/bio-mocha/bcftools-1.14/plugins/ |
| H A D | remove-overlaps.c | 148 bcf_sr_t *sr = bcf_sr_get_reader(args->sr, 0); in process()
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| /dports/biology/bcftools/bcftools-1.14/plugins/ |
| H A D | remove-overlaps.c | 148 bcf_sr_t *sr = bcf_sr_get_reader(args->sr, 0); in process()
|