| /dports/biology/py-pysam/pysam-0.18.0/samtools/ |
| H A D | bam_reheader.c | 47 const char *arg_list, int no_pg, int skip_header) in bam_reheader()
121 int cram_reheader(cram_fd *in, sam_hdr_t *h, const char *arg_list, int no_pg) in cram_reheader()
186 int no_pg) in cram_reheader_inplace2()
283 int no_pg) in cram_reheader_inplace3()
421 int no_pg) in cram_reheader_inplace()
536 int inplace = 0, r, no_pg = 0, c, skip_header = 0; in main_reheader() local
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| H A D | bam_reheader.c.pysam.c | 49 const char *arg_list, int no_pg, int skip_header) in bam_reheader()
123 int cram_reheader(cram_fd *in, sam_hdr_t *h, const char *arg_list, int no_pg) in cram_reheader()
188 int no_pg) in cram_reheader_inplace2()
285 int no_pg) in cram_reheader_inplace3()
423 int no_pg) in cram_reheader_inplace()
538 int inplace = 0, r, no_pg = 0, c, skip_header = 0; in samtools_main_reheader() local
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| H A D | bam_cat.c | 199 …const *fn, const sam_hdr_t *h, const char* outcram, sam_global_args *ga, char *arg_list, int no_pg) in cram_cat()
333 int bam_cat(int nfn, char * const *fn, sam_hdr_t *h, const char* outbam, char *arg_list, int no_pg) in bam_cat()
462 int c, ret = 0, no_pg = 0, usage = 0; in main_cat() local
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| H A D | bam_cat.c.pysam.c | 201 …const *fn, const sam_hdr_t *h, const char* outcram, sam_global_args *ga, char *arg_list, int no_pg) in cram_cat()
335 int bam_cat(int nfn, char * const *fn, sam_hdr_t *h, const char* outbam, char *arg_list, int no_pg) in bam_cat()
464 int c, ret = 0, no_pg = 0, usage = 0; in main_cat() local
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| H A D | bam_mate.c | 257 …nt remove_reads, int proper_pair_check, int add_ct, int do_mate_scoring, char *arg_list, int no_pg) in bam_mating_core()
433 int c, remove_reads = 0, proper_pair_check = 1, add_ct = 0, res = 1, mate_score = 0, no_pg = 0; in bam_mating() local
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| H A D | bam_mate.c.pysam.c | 259 …nt remove_reads, int proper_pair_check, int add_ct, int do_mate_scoring, char *arg_list, int no_pg) in bam_mating_core()
435 int c, remove_reads = 0, proper_pair_check = 1, add_ct = 0, res = 1, mate_score = 0, no_pg = 0; in bam_mating() local
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| H A D | bamshuf.c | 184 …, const char *output_file, int fast, int store_max, sam_global_args *ga, char *arg_list, int no_pg) in bamshuf()
583 …_CLEVEL, is_stdout = 0, is_un = 0, fast_coll = 0, reads_store = 10000, ret, pre_mem = 0, no_pg = 0; in main_bamshuf() local
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| H A D | bamshuf.c.pysam.c | 186 …, const char *output_file, int fast, int store_max, sam_global_args *ga, char *arg_list, int no_pg) in bamshuf()
585 …_CLEVEL, is_stdout = 0, is_un = 0, fast_coll = 0, reads_store = 10000, ret, pre_mem = 0, no_pg = 0; in main_bamshuf() local
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| H A D | bam_sort.c | 1003 int write_index, char *arg_list, int no_pg) in bam_merge_core2()
1436 int fn_size = 0, no_pg = 0; in bam_merge() local
1632 const htsFormat *out_fmt, char *arg_list, int no_pg, in bam_merge_simple()
1952 int clear_minhash, char *arg_list, int no_pg, int write_index) in write_buffer()
2418 char *arg_list, int no_pg, int write_index) in bam_sort_core_ext()
2697 int c, nargs, is_by_qname = 0, ret, o_seen = 0, level = -1, no_pg = 0; in bam_sort() local
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| H A D | bam_sort.c.pysam.c | 1005 int write_index, char *arg_list, int no_pg) in bam_merge_core2()
1438 int fn_size = 0, no_pg = 0; in bam_merge() local
1634 const htsFormat *out_fmt, char *arg_list, int no_pg, in bam_merge_simple()
1954 int clear_minhash, char *arg_list, int no_pg, int write_index) in write_buffer()
2420 char *arg_list, int no_pg, int write_index) in bam_sort_core_ext()
2699 int c, nargs, is_by_qname = 0, ret, o_seen = 0, level = -1, no_pg = 0; in bam_sort() local
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| H A D | bam_import.c | 86 int no_pg; member
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| H A D | bam_import.c.pysam.c | 88 int no_pg; member
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| H A D | bam_md.c | 237 …id = -2, ret, is_bam_out, is_uncompressed, max_nm, is_realn, capQ, baq_flag, quiet_mode, no_pg = 0; in bam_fillmd() local
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| H A D | bam_md.c.pysam.c | 239 …id = -2, ret, is_bam_out, is_uncompressed, max_nm, is_realn, capQ, baq_flag, quiet_mode, no_pg = 0; in bam_fillmd() local
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| H A D | bam_addrprg.c | 50 int no_pg; member
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| H A D | bam_addrprg.c.pysam.c | 52 int no_pg; member
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| H A D | padding.c | 449 int c, compress_level = -1, is_long_help = 0, no_pg = 0; in main_pad2unpad() local
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| /dports/biology/samtools/samtools-1.14/ |
| H A D | bam_reheader.c | 47 const char *arg_list, int no_pg, int skip_header) in bam_reheader()
121 int cram_reheader(cram_fd *in, sam_hdr_t *h, const char *arg_list, int no_pg) in cram_reheader()
186 int no_pg) in cram_reheader_inplace2()
283 int no_pg) in cram_reheader_inplace3()
421 int no_pg) in cram_reheader_inplace()
536 int inplace = 0, r, no_pg = 0, c, skip_header = 0; in main_reheader() local
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| H A D | bam_cat.c | 199 …const *fn, const sam_hdr_t *h, const char* outcram, sam_global_args *ga, char *arg_list, int no_pg) in cram_cat()
333 int bam_cat(int nfn, char * const *fn, sam_hdr_t *h, const char* outbam, char *arg_list, int no_pg) in bam_cat()
462 int c, ret = 0, no_pg = 0, usage = 0; in main_cat() local
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| H A D | bam_mate.c | 257 …nt remove_reads, int proper_pair_check, int add_ct, int do_mate_scoring, char *arg_list, int no_pg) in bam_mating_core()
433 int c, remove_reads = 0, proper_pair_check = 1, add_ct = 0, res = 1, mate_score = 0, no_pg = 0; in bam_mating() local
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| H A D | bamshuf.c | 184 …, const char *output_file, int fast, int store_max, sam_global_args *ga, char *arg_list, int no_pg) in bamshuf()
583 …_CLEVEL, is_stdout = 0, is_un = 0, fast_coll = 0, reads_store = 10000, ret, pre_mem = 0, no_pg = 0; in main_bamshuf() local
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| H A D | bam_sort.c | 1003 int write_index, char *arg_list, int no_pg) in bam_merge_core2()
1436 int fn_size = 0, no_pg = 0; in bam_merge() local
1632 const htsFormat *out_fmt, char *arg_list, int no_pg, in bam_merge_simple()
1952 int clear_minhash, char *arg_list, int no_pg, int write_index) in write_buffer()
2418 char *arg_list, int no_pg, int write_index) in bam_sort_core_ext()
2697 int c, nargs, is_by_qname = 0, ret, o_seen = 0, level = -1, no_pg = 0; in bam_sort() local
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| H A D | bam_import.c | 86 int no_pg; member
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| H A D | bam_md.c | 237 …id = -2, ret, is_bam_out, is_uncompressed, max_nm, is_realn, capQ, baq_flag, quiet_mode, no_pg = 0; in bam_fillmd() local
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| H A D | bam_addrprg.c | 50 int no_pg; member
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