| /dports/biology/freebayes/freebayes-1.3.5/scripts/ |
| H A D | fasta_generate_regions.py | 20 chrom_name = fields[0] variable
28 print(chrom_name + ":" + str(region_start) + "-" + str(end))
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| /dports/biology/py-deeptools/deepTools-3.5.1/deeptools/ |
| H A D | getScorePerBigWigBin.py | 168 for chrom_name, size in _names_and_size:
169 if chrom_name.startswith('chr'):
170 _corr_names_size.add((chrom_name[3:], size))
172 _corr_names_size.add(('chr' + chrom_name, size))
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| H A D | utilities.py | 197 for chrom_name, size in _names_and_size:
198 if chrom_name.startswith('chr'):
199 _corr_names_size.add((chrom_name[3:], size))
201 _corr_names_size.add(('chr' + chrom_name, size))
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| H A D | getScaleFactor.py | 154 …chrom_sizes = [(chrom_name, bam_handle.lengths[idx]) for idx, chrom_name in enumerate(bam_handle.r…
155 if chrom_name not in args.ignoreForNormalization]
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| /dports/biology/bedtools/bedtools2-2.30.0/src/utils/FileRecordTools/Records/ |
| H A D | Bed4Interval.cpp | 23 inline void print_record(const string& chrom_name, CHRPOS start, CHRPOS end, const string& name, st… in print_record() argument
25 …snprintf(buffer, sizeof(buffer), "%s\t%" PRId_CHRPOS "\t%" PRId_CHRPOS"\t%s", chrom_name.c_str(), … in print_record()
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| H A D | BedGraphInterval.cpp | 23 inline void print_record(const string& chrom_name, CHRPOS start, CHRPOS end, const string& name, st… in print_record() argument
25 …snprintf(buffer, sizeof(buffer), "%s\t%" PRId_CHRPOS "\t%" PRId_CHRPOS"\t%s", chrom_name.c_str(), … in print_record()
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| H A D | Bed5Interval.cpp | 24 inline void print_record(const string& chrom_name, CHRPOS start, CHRPOS end, const string& name, co… in print_record() argument
26 …snprintf(buffer, sizeof(buffer), "%s\t%" PRId_CHRPOS "\t%" PRId_CHRPOS"\t%s\t%s", chrom_name.c_str… in print_record()
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| H A D | Bed6Interval.cpp | 26 inline void print_record(const string& chrom_name, CHRPOS start, CHRPOS end, const string& name, co… in print_record() argument
28 …snprintf(buffer, sizeof(buffer), "%s\t%" PRId_CHRPOS "\t%" PRId_CHRPOS"\t%s\t%s\t%s", chrom_name.c… in print_record()
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| /dports/biology/plink/plink-ng-79b2df8c/1.9/ |
| H A D | plink_common.h | 2271 int32_t get_chrom_code(const char* chrom_name, const Chrom_info* chrom_info_ptr, uint32_t name_slen…
2276 …2_t get_chrom_code_counted(const Chrom_info* chrom_info_ptr, uint32_t name_slen, char* chrom_name);
2279 HEADER_INLINE int32_t get_chrom_code_destructive(const Chrom_info* chrom_info_ptr, char* chrom_name… in get_chrom_code_destructive() argument
2280 char* chrom_token_end = token_endnn(chrom_name); in get_chrom_code_destructive()
2282 return get_chrom_code(chrom_name, chrom_info_ptr, (uintptr_t)(chrom_token_end - chrom_name)); in get_chrom_code_destructive()
2302 int32_t try_to_add_chrom_name(const char* chrom_name, const char* file_descrip, uintptr_t line_idx,…
2304 HEADER_INLINE int32_t get_or_add_chrom_code(const char* chrom_name, const char* file_descrip, uintp… in get_or_add_chrom_code() argument
2305 *chrom_idx_ptr = get_chrom_code(chrom_name, chrom_info_ptr, name_slen); in get_or_add_chrom_code()
2309 …return try_to_add_chrom_name(chrom_name, file_descrip, line_idx, name_slen, allow_extra_chroms, ch… in get_or_add_chrom_code()
2312 …* file_descrip, uintptr_t line_idx, uint32_t allow_extra_chroms, char* chrom_name, char* chrom_nam… in get_or_add_chrom_code_destructive() argument
[all …]
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| H A D | plink_common.c | 4335 const uint32_t hashval = murmurhash3_32(chrom_name, name_slen) % CHROM_NAME_HTABLE_SIZE; in nonstd_chrom_name_htable_find()
4750 const int32_t chrom_code_raw = get_chrom_code_raw(chrom_name); in get_chrom_code()
4769 char* s_end = &(chrom_name[name_slen]); in get_chrom_code_counted()
4772 const int32_t retval = get_chrom_code(chrom_name, chrom_info_ptr, name_slen); in get_chrom_code_counted()
4794 const int32_t raw_code = get_chrom_code_raw(chrom_name); in chrom_error()
4799 LOGERRPRINTFWW("Error: Invalid chromosome code '%s' in %s.\n", chrom_name, file_descrip); in chrom_error()
4821 chrom_error(chrom_name, file_descrip, chrom_info_ptr, line_idx, *chrom_idx_ptr); in try_to_add_chrom_name()
4827 if (chrom_name[0] == '#') { in try_to_add_chrom_name()
4864 if (!strcmp(chrom_name, name_stack_ptr->ss)) { in try_to_add_chrom_name()
4876 memcpy(nonstd_names[chrom_code_end], chrom_name, name_slen + 1); in try_to_add_chrom_name()
[all …]
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| /dports/biology/mapm3/mapm3-3.0_1/mapm/ |
| H A D | sequence.c | 818 char *rest, chrom_name[99]; local
842 sf(chrom_name,"%s: ",chrom2str(current_chrom));
843 strins(maybe_seq,chrom_name);
857 char *rest, chrom_name[99]; local
868 sf(chrom_name,"%s: ",chrom2str(current_chrom));
869 strins(rest,chrom_name);
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| /dports/biology/cufflinks/cufflinks-2.2.1-89-gdc3b0cb/src/ |
| H A D | hits.cpp | 1105 string chrom_name = locus_tag.substr(0, idx); in inspect_header() local
1106 …rt.get_id(chrom_name.c_str(), NULL); // make sure the chromosome names are added to the RefSequenc… in inspect_header()
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