| /dports/biology/hisat2/hisat2-2.2.1/ |
| H A D | dp_framer.h | 137 int64_t reflen, // length of reference sequence aligned to
157 int64_t reflen, // length of reference sequence aligned to in frameFindMateRect() argument
172 reflen, in frameFindMateRect()
185 reflen, in frameFindMateRect()
206 int64_t reflen, // length of reference sequence aligned to
226 int64_t reflen, // length of reference sequence aligned to
242 size_t reflen, // in: length of reference sequence aligned to in trimToRef() argument
252 if(refr >= (int64_t)reflen) { in trimToRef()
253 trimdn = (size_t)(refr - reflen + 1); in trimToRef()
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| H A D | dp_framer.cpp | 93 assert_gt(reflen, 0); in frameSeedExtensionRect()
110 if(refr >= reflen + maxns) { in frameSeedExtensionRect()
111 trimr = (size_t)(refr - (reflen + maxns - 1)); in frameSeedExtensionRect()
197 assert_gt(reflen, 0); in frameFindMateAnchorLeftRect()
226 if(refr >= reflen + maxns) { in frameFindMateAnchorLeftRect()
227 trimr = (size_t)(refr - (reflen + maxns - 1)); in frameFindMateAnchorLeftRect()
311 assert_gt(reflen, 0); in frameFindMateAnchorRightRect()
339 if(refr >= reflen + maxns) { in frameFindMateAnchorRightRect()
340 trimr = (size_t)(refr - (reflen + maxns - 1)); in frameFindMateAnchorRightRect()
372 size_t reflen, in testCaseFindMateAnchorLeft() argument
[all …]
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| /dports/biology/bowtie2/bowtie2-2.4.4/ |
| H A D | dp_framer.h | 142 int64_t reflen, // length of reference sequence aligned to
162 int64_t reflen, // length of reference sequence aligned to in frameFindMateRect() argument
177 reflen, in frameFindMateRect()
190 reflen, in frameFindMateRect()
211 int64_t reflen, // length of reference sequence aligned to
231 int64_t reflen, // length of reference sequence aligned to
247 size_t reflen, // in: length of reference sequence aligned to in trimToRef() argument
257 if(refr >= (int64_t)reflen) { in trimToRef()
258 trimdn = (size_t)(refr - reflen + 1); in trimToRef()
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| H A D | dp_framer.cpp | 92 assert_gt(reflen, 0); in frameSeedExtensionRect()
109 if(refr >= reflen + maxns) { in frameSeedExtensionRect()
110 trimr = (size_t)(refr - (reflen + maxns - 1)); in frameSeedExtensionRect()
196 assert_gt(reflen, 0); in frameFindMateAnchorLeftRect()
225 if(refr >= reflen + maxns) { in frameFindMateAnchorLeftRect()
226 trimr = (size_t)(refr - (reflen + maxns - 1)); in frameFindMateAnchorLeftRect()
310 assert_gt(reflen, 0); in frameFindMateAnchorRightRect()
338 if(refr >= reflen + maxns) { in frameFindMateAnchorRightRect()
339 trimr = (size_t)(refr - (reflen + maxns - 1)); in frameFindMateAnchorRightRect()
371 size_t reflen, in testCaseFindMateAnchorLeft() argument
[all …]
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| /dports/games/ktuberling/ktuberling-21.12.3/po/cmake_modules/ |
| H A D | resolve-sr-hybrid | 229 my $reflen = length($ijkfrm);
230 $reflen_max = $reflen if $reflen_max < $reflen;
231 $reflen_min = $reflen if $reflen_min > $reflen;
285 my $reflen = $reflen_min;
287 while ($reflen <= $reflen_max and !$ekvfrm) {
288 $ijkfrm = substr($text, $p, $reflen);
290 $reflen += 1;
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| /dports/devel/lokalize/lokalize-21.12.3/po/cmake_modules/ |
| H A D | resolve-sr-hybrid | 229 my $reflen = length($ijkfrm);
230 $reflen_max = $reflen if $reflen_max < $reflen;
231 $reflen_min = $reflen if $reflen_min > $reflen;
285 my $reflen = $reflen_min;
287 while ($reflen <= $reflen_max and !$ekvfrm) {
288 $ijkfrm = substr($text, $p, $reflen);
290 $reflen += 1;
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| /dports/misc/kdeedu-data/kdeedu-data-21.12.3/po/cmake_modules/ |
| H A D | resolve-sr-hybrid | 229 my $reflen = length($ijkfrm);
230 $reflen_max = $reflen if $reflen_max < $reflen;
231 $reflen_min = $reflen if $reflen_min > $reflen;
285 my $reflen = $reflen_min;
287 while ($reflen <= $reflen_max and !$ekvfrm) {
288 $ijkfrm = substr($text, $p, $reflen);
290 $reflen += 1;
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| /dports/mail/mailutils/mailutils-3.13/imap4d/ |
| H A D | list.c | 61 size_t reflen; /* Length of the original reference */ member
80 if (refinfo->reflen == 0 && mu_c_strcasecmp (name, "INBOX") == 0) in list_fun()
99 size = strlen (name) + refinfo->reflen + 2; in list_fun()
116 memcpy (refinfo->buf, refinfo->refptr, refinfo->reflen); in list_fun()
117 p = refinfo->buf + refinfo->reflen; in list_fun()
210 refinfo.reflen = strlen (ref); in list_ref()
214 if (ref[refinfo.reflen-1] != pfx->delim && strcmp (ref, pfx->prefix)) in list_ref()
341 size_t reflen = strlen (ref); in imap4d_list() local
342 size_t len = i + reflen; in imap4d_list()
345 memcpy (ref + reflen, wcard, i - 1); /* omit the trailing / */ in imap4d_list()
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| /dports/biology/vcftools/vcftools-0.1.16/src/perl/ |
| H A D | fill-fs | 141 my $reflen = length($ref);
143 my $to = $pos+($reflen-1)+$$opts{length};
147 my $reflen_ori = $reflen;
153 $reflen = abs($len);
161 $reflen = $off-1;
164 substr($seq,$seq_pos,$reflen,"[$ref/$alt]");
165 if ( $reflen_ori - $reflen > 0 )
168 $seq = substr($seq,$reflen_ori-$reflen);
188 my $reflen = length($$m{ref});
189 if ( $$m{chr} ne $chr or $$m{pos}+$reflen<$from or $$m{pos}>$to ) { next; }
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| /dports/devel/git-svn/git-2.34.1/builtin/ |
| H A D | show-ref.c | 64 int reflen = strlen(refname); in show_ref() local
68 if (len > reflen) in show_ref()
70 if (memcmp(m, refname + reflen - len, len)) in show_ref()
72 if (len == reflen) in show_ref()
74 if (refname[reflen - len - 1] == '/') in show_ref()
126 int reflen = buf + len - ref; in exclude_existing() local
127 if (reflen < matchlen) in exclude_existing()
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| /dports/devel/git-p4/git-2.34.1/builtin/ |
| H A D | show-ref.c | 64 int reflen = strlen(refname); in show_ref() local
68 if (len > reflen) in show_ref()
70 if (memcmp(m, refname + reflen - len, len)) in show_ref()
72 if (len == reflen) in show_ref()
74 if (refname[reflen - len - 1] == '/') in show_ref()
126 int reflen = buf + len - ref; in exclude_existing() local
127 if (reflen < matchlen) in exclude_existing()
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| /dports/devel/git/git-2.34.1/builtin/ |
| H A D | show-ref.c | 64 int reflen = strlen(refname); in show_ref() local
68 if (len > reflen) in show_ref()
70 if (memcmp(m, refname + reflen - len, len)) in show_ref()
72 if (len == reflen) in show_ref()
74 if (refname[reflen - len - 1] == '/') in show_ref()
126 int reflen = buf + len - ref; in exclude_existing() local
127 if (reflen < matchlen) in exclude_existing()
|
| /dports/devel/git-gui/git-2.34.1/builtin/ |
| H A D | show-ref.c | 64 int reflen = strlen(refname); in show_ref() local
68 if (len > reflen) in show_ref()
70 if (memcmp(m, refname + reflen - len, len)) in show_ref()
72 if (len == reflen) in show_ref()
74 if (refname[reflen - len - 1] == '/') in show_ref()
126 int reflen = buf + len - ref; in exclude_existing() local
127 if (reflen < matchlen) in exclude_existing()
|
| /dports/devel/git-cvs/git-2.34.1/builtin/ |
| H A D | show-ref.c | 64 int reflen = strlen(refname); in show_ref() local
68 if (len > reflen) in show_ref()
70 if (memcmp(m, refname + reflen - len, len)) in show_ref()
72 if (len == reflen) in show_ref()
74 if (refname[reflen - len - 1] == '/') in show_ref()
126 int reflen = buf + len - ref; in exclude_existing() local
127 if (reflen < matchlen) in exclude_existing()
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| /dports/devel/cgit/cgit-1.2.3/git/builtin/ |
| H A D | show-ref.c | 64 int reflen = strlen(refname); in show_ref() local
68 if (len > reflen) in show_ref()
70 if (memcmp(m, refname + reflen - len, len)) in show_ref()
72 if (len == reflen) in show_ref()
74 if (refname[reflen - len - 1] == '/') in show_ref()
126 int reflen = buf + len - ref; in exclude_existing() local
127 if (reflen < matchlen) in exclude_existing()
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| /dports/biology/bcftools/bcftools-1.14/plugins/ |
| H A D | allele-length.c | 34 static uint64_t reflen[MAXLEN]; variable
79 reflen[i] = 0; in init()
92 reflen[rl] += 1; in process()
110 …printf("%d\t%"PRIu64"\t%"PRIu64"\t%"PRIu64"\t%"PRIu64"\n", i, reflen[i], altlen[i], refaltlen[i], … in destroy()
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| /dports/biology/bio-mocha/bcftools-1.14/plugins/ |
| H A D | allele-length.c | 34 static uint64_t reflen[MAXLEN]; variable
79 reflen[i] = 0; in init()
92 reflen[rl] += 1; in process()
110 …printf("%d\t%"PRIu64"\t%"PRIu64"\t%"PRIu64"\t%"PRIu64"\n", i, reflen[i], altlen[i], refaltlen[i], … in destroy()
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| /dports/devel/gdcm/gdcm-3.0.10/Testing/Source/MediaStorageAndFileFormat/Cxx/ |
| H A D | TestFileStreamer1.cxx | 110 int reflen = 0; in TestFileStream1() local
113 reflen = 384; in TestFileStream1()
117 reflen = 1000; in TestFileStream1()
119 if( vl != reflen ) in TestFileStream1()
121 … std::cerr << "Wrong length for: " << check << ":" << vl << " should be :" << reflen << std::endl; in TestFileStream1()
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| /dports/print/texinfo/texinfo-6.8/info/ |
| H A D | footnotes.c | 80 int reflen = strlen ("-Footnotes") + strlen (node->nodename); in make_footnotes_node() local
82 refname = xmalloc (reflen + 1); in make_footnotes_node()
93 (strncmp (refs[i]->nodename, refname, reflen - 1) == 0 && in make_footnotes_node()
94 refs[i]->nodename[reflen - 1] == '-' && in make_footnotes_node()
95 isdigit (refs[i]->nodename[reflen])))) in make_footnotes_node()
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| /dports/emulators/mess/mame-mame0226/3rdparty/libflac/src/metaflac/ |
| H A D | operations_shorthand_cuesheet.c | 181 size_t reflen; in export_cs_to() local
197 reflen = strlen(filename) + 7 + 1; in export_cs_to()
198 if(0 == (ref = malloc(reflen))) { in export_cs_to()
204 _snprintf(ref, reflen, "\"%s\" FLAC", filename); in export_cs_to()
206 snprintf(ref, reflen, "\"%s\" FLAC", filename); in export_cs_to()
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| /dports/emulators/mame/mame-mame0226/3rdparty/libflac/src/metaflac/ |
| H A D | operations_shorthand_cuesheet.c | 181 size_t reflen; in export_cs_to() local
197 reflen = strlen(filename) + 7 + 1; in export_cs_to()
198 if(0 == (ref = malloc(reflen))) { in export_cs_to()
204 _snprintf(ref, reflen, "\"%s\" FLAC", filename); in export_cs_to()
206 snprintf(ref, reflen, "\"%s\" FLAC", filename); in export_cs_to()
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| /dports/security/p11-kit/p11-kit-0.24.0/trust/ |
| H A D | test-trust.c | 211 long reflen; in test_check_file_msg() local
213 refdata = read_file (file, line, function, reference, &reflen); in test_check_file_msg()
214 test_check_data_msg (file, line, function, directory, name, refdata, reflen); in test_check_file_msg()
225 long reflen) in test_check_data_msg() argument
236 if (filelen != reflen || memcmp (filedata, refdata, reflen) != 0) in test_check_data_msg()
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| /dports/net/isc-dhcp44-client/dhcp-4.4.2-P1/common/tests/ |
| H A D | ns_name_test.c | 37 struct data_string* list2, const char *refbuf, size_t reflen);
146 struct data_string* list2, const char *refbuf, size_t reflen) in concat_lists() argument
156 ATF_REQUIRE_MSG(result.len == reflen, "%s result len: %d incorrect", in concat_lists()
160 ATF_REQUIRE_MSG((memcmp(result.data, refbuf, reflen) == 0), in concat_lists()
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| /dports/net/isc-dhcp44-relay/dhcp-4.4.2-P1/common/tests/ |
| H A D | ns_name_test.c | 37 struct data_string* list2, const char *refbuf, size_t reflen);
146 struct data_string* list2, const char *refbuf, size_t reflen) in concat_lists() argument
156 ATF_REQUIRE_MSG(result.len == reflen, "%s result len: %d incorrect", in concat_lists()
160 ATF_REQUIRE_MSG((memcmp(result.data, refbuf, reflen) == 0), in concat_lists()
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| /dports/net/isc-dhcp44-server/dhcp-4.4.2-P1/common/tests/ |
| H A D | ns_name_test.c | 37 struct data_string* list2, const char *refbuf, size_t reflen);
146 struct data_string* list2, const char *refbuf, size_t reflen) in concat_lists() argument
156 ATF_REQUIRE_MSG(result.len == reflen, "%s result len: %d incorrect", in concat_lists()
160 ATF_REQUIRE_MSG((memcmp(result.data, refbuf, reflen) == 0), in concat_lists()
|