| /dports/biology/freebayes/freebayes-1.3.5/contrib/htslib/htslib/ |
| H A D | faidx.h | 226 char *faidx_fetch_seq(const faidx_t *fai, const char *c_name, int p_beg_i, int p_end_i, int *len);
240 char *faidx_fetch_seq64(const faidx_t *fai, const char *c_name, hts_pos_t p_beg_i, hts_pos_t p_end_…
254 char *faidx_fetch_qual(const faidx_t *fai, const char *c_name, int p_beg_i, int p_end_i, int *len);
268 char *faidx_fetch_qual64(const faidx_t *fai, const char *c_name, hts_pos_t p_beg_i, hts_pos_t p_end…
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| /dports/biology/py-pysam/pysam-0.18.0/htslib/htslib/ |
| H A D | faidx.h | 226 char *faidx_fetch_seq(const faidx_t *fai, const char *c_name, int p_beg_i, int p_end_i, int *len);
240 char *faidx_fetch_seq64(const faidx_t *fai, const char *c_name, hts_pos_t p_beg_i, hts_pos_t p_end_…
254 char *faidx_fetch_qual(const faidx_t *fai, const char *c_name, int p_beg_i, int p_end_i, int *len);
268 char *faidx_fetch_qual64(const faidx_t *fai, const char *c_name, hts_pos_t p_beg_i, hts_pos_t p_end…
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| /dports/biology/htslib/htslib-1.14/htslib/ |
| H A D | faidx.h | 226 char *faidx_fetch_seq(const faidx_t *fai, const char *c_name, int p_beg_i, int p_end_i, int *len);
240 char *faidx_fetch_seq64(const faidx_t *fai, const char *c_name, hts_pos_t p_beg_i, hts_pos_t p_end_…
254 char *faidx_fetch_qual(const faidx_t *fai, const char *c_name, int p_beg_i, int p_end_i, int *len);
268 char *faidx_fetch_qual64(const faidx_t *fai, const char *c_name, hts_pos_t p_beg_i, hts_pos_t p_end…
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| /dports/biology/seqan1/seqan-1.3.1/lib/samtools/ |
| H A D | faidx.c | 391 char *faidx_fetch_seq(const faidx_t *fai, char *c_name, int p_beg_i, int p_end_i, int *len) in faidx_fetch_seq() argument
403 if(p_end_i < p_beg_i) p_beg_i = p_end_i; in faidx_fetch_seq()
404 if(p_beg_i < 0) p_beg_i = 0; in faidx_fetch_seq()
405 else if(val.len <= p_beg_i) p_beg_i = val.len - 1; in faidx_fetch_seq()
411 seq = (char*)malloc(p_end_i - p_beg_i + 2); in faidx_fetch_seq()
412 …razf_seek(fai->rz, val.offset + p_beg_i / val.line_blen * val.line_len + p_beg_i % val.line_blen, … in faidx_fetch_seq()
413 while (razf_read(fai->rz, &c, 1) == 1 && l < p_end_i - p_beg_i + 1) in faidx_fetch_seq()
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| H A D | faidx.h | 97 char *faidx_fetch_seq(const faidx_t *fai, char *c_name, int p_beg_i, int p_end_i, int *len);
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| /dports/biology/freebayes/freebayes-1.3.5/contrib/htslib/ |
| H A D | faidx.c | 846 if(*p_end_i < *p_beg_i) in faidx_adjust_position()
847 *p_beg_i = *p_end_i; in faidx_adjust_position()
849 if(*p_beg_i < 0) in faidx_adjust_position()
850 *p_beg_i = 0; in faidx_adjust_position()
851 else if(val->len <= *p_beg_i) in faidx_adjust_position()
852 *p_beg_i = val->len - 1; in faidx_adjust_position()
867 if (faidx_adjust_position(fai, &val, c_name, &p_beg_i, &p_end_i, len)) { in faidx_fetch_seq64()
872 return fai_retrieve(fai, &val, val.seq_offset, p_beg_i, p_end_i + 1, len); in faidx_fetch_seq64()
878 char *ret = faidx_fetch_seq64(fai, c_name, p_beg_i, p_end_i, &len64); in faidx_fetch_seq()
888 if (faidx_adjust_position(fai, &val, c_name, &p_beg_i, &p_end_i, len)) { in faidx_fetch_qual64()
[all …]
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| /dports/biology/py-pysam/pysam-0.18.0/htslib/ |
| H A D | faidx.c | 846 if(*p_end_i < *p_beg_i) in faidx_adjust_position()
847 *p_beg_i = *p_end_i; in faidx_adjust_position()
849 if(*p_beg_i < 0) in faidx_adjust_position()
850 *p_beg_i = 0; in faidx_adjust_position()
851 else if(val->len <= *p_beg_i) in faidx_adjust_position()
852 *p_beg_i = val->len - 1; in faidx_adjust_position()
867 if (faidx_adjust_position(fai, &val, c_name, &p_beg_i, &p_end_i, len)) { in faidx_fetch_seq64()
872 return fai_retrieve(fai, &val, val.seq_offset, p_beg_i, p_end_i + 1, len); in faidx_fetch_seq64()
878 char *ret = faidx_fetch_seq64(fai, c_name, p_beg_i, p_end_i, &len64); in faidx_fetch_seq()
888 if (faidx_adjust_position(fai, &val, c_name, &p_beg_i, &p_end_i, len)) { in faidx_fetch_qual64()
[all …]
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| /dports/biology/htslib/htslib-1.14/ |
| H A D | faidx.c | 846 if(*p_end_i < *p_beg_i) in faidx_adjust_position()
847 *p_beg_i = *p_end_i; in faidx_adjust_position()
849 if(*p_beg_i < 0) in faidx_adjust_position()
850 *p_beg_i = 0; in faidx_adjust_position()
851 else if(val->len <= *p_beg_i) in faidx_adjust_position()
852 *p_beg_i = val->len - 1; in faidx_adjust_position()
867 if (faidx_adjust_position(fai, &val, c_name, &p_beg_i, &p_end_i, len)) { in faidx_fetch_seq64()
872 return fai_retrieve(fai, &val, val.seq_offset, p_beg_i, p_end_i + 1, len); in faidx_fetch_seq64()
878 char *ret = faidx_fetch_seq64(fai, c_name, p_beg_i, p_end_i, &len64); in faidx_fetch_seq()
888 if (faidx_adjust_position(fai, &val, c_name, &p_beg_i, &p_end_i, len)) { in faidx_fetch_qual64()
[all …]
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| /dports/biology/ugene/ugene-40.1/src/libs_3rdparty/samtools/src/samtools/ |
| H A D | faidx.c | 408 char *faidx_fetch_seq(const faidx_t *fai, char *c_name, int p_beg_i, int p_end_i, int *len) in faidx_fetch_seq() argument
420 if(p_end_i < p_beg_i) p_beg_i = p_end_i; in faidx_fetch_seq()
421 if(p_beg_i < 0) p_beg_i = 0; in faidx_fetch_seq()
422 else if(val.len <= p_beg_i) p_beg_i = val.len - 1; in faidx_fetch_seq()
428 seq = (char*)malloc(p_end_i - p_beg_i + 2); in faidx_fetch_seq()
429 …razf_seek(fai->rz, val.offset + p_beg_i / val.line_blen * val.line_len + p_beg_i % val.line_blen, … in faidx_fetch_seq()
430 while (razf_read(fai->rz, &c, 1) == 1 && l < p_end_i - p_beg_i + 1) in faidx_fetch_seq()
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| H A D | faidx.h | 97 char *faidx_fetch_seq(const faidx_t *fai, char *c_name, int p_beg_i, int p_end_i, int *len);
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| /dports/biology/stringtie/stringtie-2.1.1/samtools-0.1.18/ |
| H A D | faidx.c | 401 char *faidx_fetch_seq(const faidx_t *fai, char *c_name, int p_beg_i, int p_end_i, int *len) in faidx_fetch_seq() argument
413 if(p_end_i < p_beg_i) p_beg_i = p_end_i; in faidx_fetch_seq()
414 if(p_beg_i < 0) p_beg_i = 0; in faidx_fetch_seq()
415 else if(val.len <= p_beg_i) p_beg_i = val.len - 1; in faidx_fetch_seq()
421 seq = (char*)malloc(p_end_i - p_beg_i + 2); in faidx_fetch_seq()
422 …razf_seek(fai->rz, val.offset + p_beg_i / val.line_blen * val.line_len + p_beg_i % val.line_blen, … in faidx_fetch_seq()
423 while (razf_read(fai->rz, &c, 1) == 1 && l < p_end_i - p_beg_i + 1) in faidx_fetch_seq()
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| H A D | faidx.h | 97 char *faidx_fetch_seq(const faidx_t *fai, char *c_name, int p_beg_i, int p_end_i, int *len);
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| /dports/biology/bedtools/bedtools2-2.30.0/src/utils/htslib/ |
| H A D | faidx.c | 877 if(*p_end_i < *p_beg_i) in faidx_adjust_position()
878 *p_beg_i = *p_end_i; in faidx_adjust_position()
880 if(*p_beg_i < 0) in faidx_adjust_position()
881 *p_beg_i = 0; in faidx_adjust_position()
882 else if(val->len <= *p_beg_i) in faidx_adjust_position()
883 *p_beg_i = val->len - 1; in faidx_adjust_position()
894 char *faidx_fetch_seq(const faidx_t *fai, const char *c_name, int p_beg_i, int p_end_i, int *len) in faidx_fetch_seq() argument
899 if (faidx_adjust_position(fai, &val, c_name, &p_beg_i, &p_end_i, len)) { in faidx_fetch_seq()
904 return fai_retrieve(fai, &val, val.seq_offset, p_beg_i, (long) p_end_i + 1, len); in faidx_fetch_seq()
913 if (faidx_adjust_position(fai, &val, c_name, &p_beg_i, &p_end_i, len)) { in faidx_fetch_qual()
[all …]
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| /dports/biology/vt/vt-0.57721/lib/htslib/ |
| H A D | faidx.c | 564 char *faidx_fetch_seq(const faidx_t *fai, const char *c_name, int p_beg_i, int p_end_i, int *len) in faidx_fetch_seq() argument
578 if(p_end_i < p_beg_i) p_beg_i = p_end_i; in faidx_fetch_seq()
579 if(p_beg_i < 0) p_beg_i = 0; in faidx_fetch_seq()
580 else if(val.len <= p_beg_i) p_beg_i = val.len - 1; in faidx_fetch_seq()
585 return fai_retrieve(fai, &val, p_beg_i, (long) p_end_i + 1, len); in faidx_fetch_seq()
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| /dports/biology/stacks/stacks-2.4/htslib/ |
| H A D | faidx.c | 564 char *faidx_fetch_seq(const faidx_t *fai, const char *c_name, int p_beg_i, int p_end_i, int *len) in faidx_fetch_seq() argument
578 if(p_end_i < p_beg_i) p_beg_i = p_end_i; in faidx_fetch_seq()
579 if(p_beg_i < 0) p_beg_i = 0; in faidx_fetch_seq()
580 else if(val.len <= p_beg_i) p_beg_i = val.len - 1; in faidx_fetch_seq()
585 return fai_retrieve(fai, &val, p_beg_i, (long) p_end_i + 1, len); in faidx_fetch_seq()
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| /dports/biology/kallisto/kallisto-0.46.1/ext/htslib/ |
| H A D | faidx.c | 600 char *faidx_fetch_seq(const faidx_t *fai, const char *c_name, int p_beg_i, int p_end_i, int *len) in faidx_fetch_seq() argument
614 if(p_end_i < p_beg_i) p_beg_i = p_end_i; in faidx_fetch_seq()
615 if(p_beg_i < 0) p_beg_i = 0; in faidx_fetch_seq()
616 else if(val.len <= p_beg_i) p_beg_i = val.len - 1; in faidx_fetch_seq()
621 return fai_retrieve(fai, &val, p_beg_i, (long) p_end_i + 1, len); in faidx_fetch_seq()
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| /dports/biology/bedtools/bedtools2-2.30.0/src/utils/htslib/htslib/ |
| H A D | faidx.h | 197 char *faidx_fetch_seq(const faidx_t *fai, const char *c_name, int p_beg_i, int p_end_i, int *len);
210 char *faidx_fetch_qual(const faidx_t *fai, const char *c_name, int p_beg_i, int p_end_i, int *len);
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| /dports/biology/vt/vt-0.57721/ |
| H A D | hts_utils.cpp | 41 char *faidx_fetch_uc_seq(const faidx_t *fai, const char *c_name, int p_beg_i, int p_end_i, int *len) in faidx_fetch_uc_seq() argument
53 if(p_end_i < p_beg_i) p_beg_i = p_end_i; in faidx_fetch_uc_seq()
54 if(p_beg_i < 0) p_beg_i = 0; in faidx_fetch_uc_seq()
55 else if(val.len <= p_beg_i) p_beg_i = val.len - 1; in faidx_fetch_uc_seq()
60 …int ret = bgzf_useek(fai->bgzf, val.offset + p_beg_i / val.line_blen * val.line_len + p_beg_i % va… in faidx_fetch_uc_seq()
68 seq = (char*)malloc(p_end_i - p_beg_i + 2); in faidx_fetch_uc_seq()
69 while ( (c=bgzf_getc(fai->bgzf))>=0 && l < p_end_i - p_beg_i + 1) in faidx_fetch_uc_seq()
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| H A D | hts_utils.h | 60 char *faidx_fetch_uc_seq(const faidx_t *fai, const char *c_name, int p_beg_i, int p_end_i, int *len…
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| /dports/biology/vt/vt-0.57721/lib/htslib/htslib/ |
| H A D | faidx.h | 137 char *faidx_fetch_seq(const faidx_t *fai, const char *c_name, int p_beg_i, int p_end_i, int *len);
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| /dports/biology/stacks/stacks-2.4/htslib/htslib/ |
| H A D | faidx.h | 137 char *faidx_fetch_seq(const faidx_t *fai, const char *c_name, int p_beg_i, int p_end_i, int *len);
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| /dports/biology/kallisto/kallisto-0.46.1/ext/htslib/htslib/ |
| H A D | faidx.h | 137 char *faidx_fetch_seq(const faidx_t *fai, const char *c_name, int p_beg_i, int p_end_i, int *len);
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| /dports/biology/py-pysam/pysam-0.18.0/pysam/ |
| H A D | libchtslib.pxd | 1319 # @param p_beg_i Beginning position number (zero-based)
1328 int p_beg_i,
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