| /dports/biology/py-hits/hits-0.1/hits/ |
| H A D | fastq.py | 309 def get_read_name_parser(read_name): argument
310 if read_name.startswith('test'):
314 elif read_name.startswith('SRR'):
319 elif read_name.startswith('ERR') or read_name.startswith('DRR'):
326 if '#' in read_name:
328 elif '/' in read_name:
342 def standardizer(read_name): argument
347 def standardizer(read_name): argument
352 def standardizer(read_name): argument
391 def parse_SRA_read_name(read_name): argument
[all …]
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| /dports/biology/subread/subread-2.0.2-source/src/ |
| H A D | propmapped.c | 268 int rname_len = strlen(read_name); in add_read_flags()
272 if(read_name[x1]=='/'){ in add_read_flags()
273 read_name[x1]=0; in add_read_flags()
281 strcat(read_name, (flags&0x40)?"!!_1":"!!_2"); in add_read_flags()
284 rname_len = strlen(read_name); in add_read_flags()
292 wlen = fwrite(read_name,rname_len,1,fp); in add_read_flags()
384 char * read_name; in prop_PE() local
388 read_name = malloc((int)read_len+1); in prop_PE()
389 retvv = fread(read_name,read_len,1,fp); in prop_PE()
391 read_name[read_len]=0; in prop_PE()
[all …]
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| /dports/biology/bowtie/bowtie-1.3.1/scripts/ |
| H A D | reconcile_alignments_pe.pl | 181 my $read_name = $name1s[0];
187 if(defined($num_hash{$read_name})) {
188 $num_hash{$read_name}++;
191 $num_hash{$read_name} = 1;
195 if($num_hash{$read_name} > $khits) {
199 if($num_hash{$read_name} > $m) {
203 defined($hits_hash{$read_name}) &&
233 $hits_hash{$read_name}{seq1} = $seq1;
235 $hits_hash{$read_name}{seq2} = $seq2;
238 $hits_hash{$read_name}{seq1} = $seq2;
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| /dports/biology/subread/subread-2.0.2-source/test/subread-align/ |
| H A D | readname_ora_match.py | 19 read_name = linfo[0]
42 if read_name.find ('/')>0:
43 name_info = read_name.split('/')
46 if read_name.find ('/')>0:
47 name_info = read_name.rsplit('_',5)
49 name_info = read_name.rsplit('_',5)
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| H A D | readname_cigar_match.py | 27 read_name = fls[0] variable
34 oracle_info = read_name.split('_')
75 print "%s,%d\t%s,%d\t\t%s"%(chro, chro_pos, oracle_chro, oracle_pos, read_name)
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| /dports/audio/jack_umidi/jack_umidi-1.1.1/ |
| H A D | jack_umidi.c | 67 static char *read_name; variable
462 if (read_name != NULL && read_fd == -1) in umidi_kill_on_close()
472 if (read_name == NULL) { in umidi_watchdog_sub()
574 free(read_name); in main()
576 read_name = strdup(optarg); in main()
584 free(read_name); in main()
585 read_name = strdup(optarg); in main()
620 if (read_name != NULL) { in main()
622 pname = read_name + 5; in main()
625 pname = read_name; in main()
[all …]
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| /dports/emulators/mess/mame-mame0226/src/emu/ |
| H A D | addrmap.h | 188 address_map_entry &r(Ret (T::*read)(Params...), const char *read_name) in r() argument
189 { return r(emu::detail::make_delegate(*make_pointer<T>(m_devbase), read, read_name)); } in r()
206 address_map_entry &r(const char *tag, Ret (T::*read)(Params...), const char *read_name) in r() argument
207 { return r(emu::detail::make_delegate(m_devbase, tag, read, read_name)); } in r()
224 address_map_entry &r(T &obj, Ret (U::*read)(Params...), const char *read_name) in r() argument
225 { return r(emu::detail::make_delegate(*make_pointer<U>(obj), read, read_name)); } in r()
242 …ss_map_entry &r(device_finder<T, Reqd> &finder, Ret (U::*read)(Params...), const char *read_name) { in r() argument
244 return r(emu::detail::make_delegate(device, DEVICE_SELF, read, read_name)); in r()
250 return r(emu::detail::make_delegate(device, DEVICE_SELF, read, read_name)); in r()
268 return r(emu::detail::make_delegate(device, DEVICE_SELF, read, read_name)) in rw()
[all …]
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| /dports/emulators/mame/mame-mame0226/src/emu/ |
| H A D | addrmap.h | 188 address_map_entry &r(Ret (T::*read)(Params...), const char *read_name) in r() argument
189 { return r(emu::detail::make_delegate(*make_pointer<T>(m_devbase), read, read_name)); } in r()
206 address_map_entry &r(const char *tag, Ret (T::*read)(Params...), const char *read_name) in r() argument
207 { return r(emu::detail::make_delegate(m_devbase, tag, read, read_name)); } in r()
224 address_map_entry &r(T &obj, Ret (U::*read)(Params...), const char *read_name) in r() argument
225 { return r(emu::detail::make_delegate(*make_pointer<U>(obj), read, read_name)); } in r()
242 …ss_map_entry &r(device_finder<T, Reqd> &finder, Ret (U::*read)(Params...), const char *read_name) { in r() argument
244 return r(emu::detail::make_delegate(device, DEVICE_SELF, read, read_name)); in r()
250 return r(emu::detail::make_delegate(device, DEVICE_SELF, read, read_name)); in r()
268 return r(emu::detail::make_delegate(device, DEVICE_SELF, read, read_name)) in rw()
[all …]
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| /dports/biology/stacks/stacks-2.4/src/ |
| H A D | utils.h | 334 void strip_read_number(string& read_name) { in strip_read_number() argument
335 if (read_name.size() >= 2) { in strip_read_number()
337 if ((*read_name.rbegin() == '1' || *read_name.rbegin() == '2') in strip_read_number()
338 && (*++read_name.rbegin() == '/' || *++read_name.rbegin() == '_') in strip_read_number()
341 read_name.resize(read_name.size()-2); in strip_read_number()
346 if ((p = q = strchr(read_name.c_str(), ' ')) != NULL) { in strip_read_number()
348 read_name.resize(p - read_name.c_str()); in strip_read_number()
354 cerr << "Error: Unrecognized paired-end read name format, at '" << read_name << "'.\n"; in strip_read_number()
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| /dports/archivers/cabextract/cabextract-1.9.1/src/ |
| H A D | cabinfo.c | 44 char *read_name();
212 printf("- prev cabinet = %s\n", read_name()); in getinfo()
213 printf("- prev disk = %s\n", read_name()); in getinfo()
216 printf("- next cabinet = %s\n", read_name()); in getinfo()
217 printf("- next disk = %s\n", read_name()); in getinfo()
301 printf(" - name = %s%s\n", read_name(), in getinfo()
326 char *read_name() { in read_name() function
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| /dports/security/tpm2-tss/tpm2-tss-3.1.0/test/integration/ |
| H A D | esys-createloaded.int.c | 27 TPM2B_NAME *read_name = NULL; in check_name() local
32 NULL, &read_name, NULL); in check_name()
38 if (read_name->size != get_name->size) { in check_name()
40 read_name->size, get_name->size); in check_name()
44 result = memcmp(read_name->name, get_name->name, get_name->size) == 0; in check_name()
47 Esys_Free(read_name); in check_name()
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| /dports/biology/py-ont-fast5-api/ont_fast5_api-release_4.0.0/ont_fast5_api/ |
| H A D | multi_fast5.py | 88 read_name = "read_" + read_to_add.read_id
89 self.handle.create_group(read_name)
90 output_group = self.handle[read_name]
118 read_name = "read_" + read_to_add.read_id
119 self.handle.create_group(read_name)
120 output_group = self.handle[read_name]
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| /dports/biology/subread/subread-2.0.2-source/src/longread-one/ |
| H A D | LRMfile-io.c | 114 int LRMgeinput_next_read(LRMgene_input_t * input, char * read_name, char * read_string, char * qual… in LRMgeinput_next_read() argument
119 if (read_name == NULL){ in LRMgeinput_next_read()
127 int retv = LRMgeinput_readline(input, LRMMAX_READ_NAME_LEN, read_name); in LRMgeinput_next_read()
131 while(read_name[cursor]) in LRMgeinput_next_read()
133 if(read_name[cursor] == ' ' || read_name[cursor] == '\t') in LRMgeinput_next_read()
135 read_name [cursor] = 0; in LRMgeinput_next_read()
159 …t, LRMthread_context_t * thread_context, unsigned int *read_len, char * read_name, char * read_tex… in LRMfetch_next_read() argument
164 this_rlen = LRMgeinput_next_read(&context -> input_file, read_name, read_text, qual_text); in LRMfetch_next_read()
280 int name_len = strlen(iteration_context -> read_name)+1; in LRMgenerate_bam_record()
287 memcpy(target_ptr+36, iteration_context->read_name, name_len); in LRMgenerate_bam_record()
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| /dports/biology/hisat2/hisat2-2.2.1/evaluation/simulation/ |
| H A D | calculate_read_cost.py | 1323 read_name = read_name[4:]
1325 if len(read_name) > 2 and read_name[-2] == '/':
1326 read_name = read_name[:-2]
1329 if read_name not in db_dic:
1330 db_dic[read_name] = []
1457 maps = db_dic[read_name]
1561 read_name = read_name[4:]
1563 if len(read_name) > 2 and read_name[-2] == '/':
1564 read_name = read_name[:-2]
1568 db_dic[read_name] = []
[all …]
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| /dports/lang/gcc12-devel/gcc-12-20211205/gcc/ |
| H A D | read-rtl-function.c | 592 read_name (&directive); in parse_insn_chain()
615 read_name (&name); in parse_block()
691 read_name (&name); in parse_bb_idx()
938 read_name (&name); in read_rtx_operand()
979 read_name (&name); in parse_enum_value()
1042 read_name (&name); in read_rtx_operand_i_or_n()
1142 read_name (&name); in extra_parsing_for_operand_code_0()
1201 read_name (&name); in extra_parsing_for_operand_code_0()
1229 read_name (&name); in handle_any_trailing_information()
1246 read_name (&name); in handle_any_trailing_information()
[all …]
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| /dports/devel/avr-gcc/gcc-10.2.0/gcc/ |
| H A D | read-rtl-function.c | 592 read_name (&directive); in parse_insn_chain()
615 read_name (&name); in parse_block()
691 read_name (&name); in parse_bb_idx()
937 read_name (&name); in read_rtx_operand()
978 read_name (&name); in parse_enum_value()
1041 read_name (&name); in read_rtx_operand_i_or_n()
1141 read_name (&name); in extra_parsing_for_operand_code_0()
1200 read_name (&name); in extra_parsing_for_operand_code_0()
1228 read_name (&name); in handle_any_trailing_information()
1245 read_name (&name); in handle_any_trailing_information()
[all …]
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| /dports/misc/cxx_atomics_pic/gcc-11.2.0/gcc/ |
| H A D | read-rtl-function.c | 592 read_name (&directive); in parse_insn_chain()
615 read_name (&name); in parse_block()
691 read_name (&name); in parse_bb_idx()
937 read_name (&name); in read_rtx_operand()
978 read_name (&name); in parse_enum_value()
1041 read_name (&name); in read_rtx_operand_i_or_n()
1141 read_name (&name); in extra_parsing_for_operand_code_0()
1200 read_name (&name); in extra_parsing_for_operand_code_0()
1228 read_name (&name); in handle_any_trailing_information()
1245 read_name (&name); in handle_any_trailing_information()
[all …]
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| /dports/lang/gcc10/gcc-10.3.0/gcc/ |
| H A D | read-rtl-function.c | 592 read_name (&directive); in parse_insn_chain()
615 read_name (&name); in parse_block()
691 read_name (&name); in parse_bb_idx()
937 read_name (&name); in read_rtx_operand()
978 read_name (&name); in parse_enum_value()
1041 read_name (&name); in read_rtx_operand_i_or_n()
1141 read_name (&name); in extra_parsing_for_operand_code_0()
1200 read_name (&name); in extra_parsing_for_operand_code_0()
1228 read_name (&name); in handle_any_trailing_information()
1245 read_name (&name); in handle_any_trailing_information()
[all …]
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| /dports/lang/gcc11-devel/gcc-11-20211009/gcc/ |
| H A D | read-rtl-function.c | 592 read_name (&directive); in parse_insn_chain()
615 read_name (&name); in parse_block()
691 read_name (&name); in parse_bb_idx()
937 read_name (&name); in read_rtx_operand()
978 read_name (&name); in parse_enum_value()
1041 read_name (&name); in read_rtx_operand_i_or_n()
1141 read_name (&name); in extra_parsing_for_operand_code_0()
1200 read_name (&name); in extra_parsing_for_operand_code_0()
1228 read_name (&name); in handle_any_trailing_information()
1245 read_name (&name); in handle_any_trailing_information()
[all …]
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| /dports/lang/gcc11/gcc-11.2.0/gcc/ |
| H A D | read-rtl-function.c | 592 read_name (&directive); in parse_insn_chain()
615 read_name (&name); in parse_block()
691 read_name (&name); in parse_bb_idx()
937 read_name (&name); in read_rtx_operand()
978 read_name (&name); in parse_enum_value()
1041 read_name (&name); in read_rtx_operand_i_or_n()
1141 read_name (&name); in extra_parsing_for_operand_code_0()
1200 read_name (&name); in extra_parsing_for_operand_code_0()
1228 read_name (&name); in handle_any_trailing_information()
1245 read_name (&name); in handle_any_trailing_information()
[all …]
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| /dports/lang/gcc10-devel/gcc-10-20211008/gcc/ |
| H A D | read-rtl-function.c | 592 read_name (&directive); in parse_insn_chain()
615 read_name (&name); in parse_block()
691 read_name (&name); in parse_bb_idx()
937 read_name (&name); in read_rtx_operand()
978 read_name (&name); in parse_enum_value()
1041 read_name (&name); in read_rtx_operand_i_or_n()
1141 read_name (&name); in extra_parsing_for_operand_code_0()
1200 read_name (&name); in extra_parsing_for_operand_code_0()
1228 read_name (&name); in handle_any_trailing_information()
1245 read_name (&name); in handle_any_trailing_information()
[all …]
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| /dports/games/widelands/widelands-build21/src/map_io/ |
| H A D | map_bob_packet.cc | 42 char const* const read_name = fr.c_string(); in read_bob() local
48 throw GameDataError("unknown legacy bob %s/%s", owner.c_str(), read_name); in read_bob()
51 const std::string name = lookup_table.lookup_critter(read_name, packet_version); in read_bob()
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| /dports/x11/roxterm/roxterm-3.11.1/src/ |
| H A D | getname.c | 109 const char *read_name = gtk_entry_get_text(GTK_ENTRY(name_field)); in getname_run_dialog() local
111 if (name_clashes(read_name, existing)) in getname_run_dialog()
125 new_name = g_strdup(read_name); in getname_run_dialog()
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| /dports/devel/zpu-gcc/zpu-toolchain-1.0/toolchain/gcc/gcc/ |
| H A D | read-rtl.c | 36 static void read_name (char *, FILE *);
155 read_name (char *str, FILE *infile) in read_name() function
444 read_name (tmp_char, infile); in read_constants()
450 read_name (tmp_char, infile); in read_constants()
545 read_name (tmp_char, infile); in read_rtx()
584 read_name (tmp_char, infile); in read_rtx()
707 read_name (tmp_char, infile); in read_rtx()
729 read_name (tmp_char, infile); in read_rtx()
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| /dports/devel/zpu-binutils/zpu-toolchain-1.0/toolchain/gcc/gcc/ |
| H A D | read-rtl.c | 36 static void read_name (char *, FILE *);
155 read_name (char *str, FILE *infile) in read_name() function
444 read_name (tmp_char, infile); in read_constants()
450 read_name (tmp_char, infile); in read_constants()
545 read_name (tmp_char, infile); in read_rtx()
584 read_name (tmp_char, infile); in read_rtx()
707 read_name (tmp_char, infile); in read_rtx()
729 read_name (tmp_char, infile); in read_rtx()
|