/dports/biology/py-crossmap/CrossMap-0.5.4/lib/cmmodule/ |
H A D | mapbam.py | 193 new_alignment.template_length = 0 #9 255 new_alignment.template_length = 0 275 new_alignment.template_length = 0 334 new_alignment.template_length = 0 352 new_alignment.template_length = 0 388 new_alignment.template_length = 0 421 new_alignment.template_length = 0 457 new_alignment.template_length = 0 470 new_alignment.template_length = 0 485 new_alignment.template_length = 0 [all …]
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/dports/biology/hhsuite/hh-suite-3.3.0/scripts/ |
H A D | hh_reader.py | 45 template_length = None 75 template_id, template_length, template_info, template_neff, 166 template_length = token_5 171 template_id, template_length, template_info, template_neff,
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/dports/devel/gnulib/gnulib-20140202-stable/build-aux/ |
H A D | mktempd | 118 template_length=`echo "$template" | wc -c` 120 nx=`expr $template_length - $nx`
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/dports/security/pkcs11-tools/pkcs11-tools-2.5.0/.gnulib/build-aux/ |
H A D | mktempd | 118 template_length=`echo "$template" | wc -c` 120 nx=`expr $template_length - $nx`
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/dports/audio/gsequencer/gsequencer-3.10.4/ags/audio/fx/ |
H A D | ags_fx_pattern_audio_signal.c | 164 guint template_length; in ags_fx_pattern_audio_signal_run_inter() local 250 template_length = 0; in ags_fx_pattern_audio_signal_run_inter() 263 "length", &template_length, in ags_fx_pattern_audio_signal_run_inter() 267 template_length = (guint) floor(delay) + 1; in ags_fx_pattern_audio_signal_run_inter()
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/dports/biology/py-deeptools/deepTools-3.5.1/deeptools/ |
H A D | getFragmentAndReadSize.py | 41 reads = np.array([(abs(r.template_length), r.infer_query_length(always=False)) 48 reads = np.array([(abs(r.template_length), r.infer_query_length(always=False))
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H A D | utilities.py | 56 if abs(read.template_length) > 0: 58 return read.template_length 59 return abs(read.template_length)
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H A D | correctGCBias.py | 138 fragStart = read.reference_end + read.template_length 139 elif read.template_length >= read.query_alignment_length: 141 fragEnd = read.pos + read.template_length
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H A D | alignmentSieve.py | 190 b2.template_length = tLen - deltaTLen 192 b2.template_length = tLen + deltaTLen
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/dports/biology/py-biopython/biopython-1.79/Bio/Blast/ |
H A D | NCBIWWW.py | 81 template_length=None, 190 ("TEMPLATE_LENGTH", template_length),
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/dports/science/apbs/apbs-pdb2pqr-apbs-1.5-102-g500c1473/pdb2pqr/propka30/Source/ |
H A D | mutate.py | 1054 template_length = calculateVectorLength(position['template']['N']) 1057 theta1 = math.asin(cross_product_length/(target_length*template_length)) 1067 template_length = calculateVectorLength(template_cross_product) 1069 theta2 = math.acos(scalar_product/(target_length*template_length)) 1071 theta2 = -math.acos(scalar_product/(target_length*template_length)) 1231 template_length = calculateVectorLength(position['template']['N']) 1234 theta1 = math.asin(cross_product_length/(target_length*template_length)) 1250 template_length = calculateVectorLength(template_cross_product) 1252 theta2 = math.acos(scalar_product/(target_length*template_length)) 1254 theta2 = -math.acos(scalar_product/(target_length*template_length))
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/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/algo/blast/unit_tests/api/ |
H A D | ntscan_unit_test.cpp | 413 scan_range[1] = subject_bases - mb_lt->template_length; in ScanOffsetTestCore() 516 scan_range[1] = subject_bases - mb_lt->template_length; in ScanMaxHitsTestCore() 586 scan_range[1] = subject_bases - mb_lt->template_length; in ScanCheckHitsCore() 817 scan_range[1] = subject_bases - mb_lt->template_length; in BOOST_FIXTURE_TEST_SUITE() 829 scan_range[1] = subject_bases - mb_lt->template_length; in BOOST_FIXTURE_TEST_SUITE()
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H A D | ntlookup_unit_test.cpp | 279 BOOST_REQUIRE_EQUAL(16, (int)lookup->template_length); in BOOST_AUTO_TEST_CASE() 325 BOOST_REQUIRE_EQUAL(16, (int)lookup->template_length); in BOOST_AUTO_TEST_CASE() 371 BOOST_REQUIRE_EQUAL(16, (int)lookup->template_length); in BOOST_AUTO_TEST_CASE() 417 BOOST_REQUIRE_EQUAL(16, (int)lookup->template_length); in BOOST_AUTO_TEST_CASE() 463 BOOST_REQUIRE_EQUAL(16, (int)lookup->template_length); in BOOST_AUTO_TEST_CASE()
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/dports/biology/ncbi-blast+/ncbi-blast-2.12.0+-src/c++/src/algo/blast/unit_tests/api/ |
H A D | ntscan_unit_test.cpp | 413 scan_range[1] = subject_bases - mb_lt->template_length; in ScanOffsetTestCore() 516 scan_range[1] = subject_bases - mb_lt->template_length; in ScanMaxHitsTestCore() 586 scan_range[1] = subject_bases - mb_lt->template_length; in ScanCheckHitsCore() 817 scan_range[1] = subject_bases - mb_lt->template_length; in BOOST_FIXTURE_TEST_SUITE() 829 scan_range[1] = subject_bases - mb_lt->template_length; in BOOST_FIXTURE_TEST_SUITE()
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H A D | ntlookup_unit_test.cpp | 279 BOOST_REQUIRE_EQUAL(16, (int)lookup->template_length); in BOOST_AUTO_TEST_CASE() 325 BOOST_REQUIRE_EQUAL(16, (int)lookup->template_length); in BOOST_AUTO_TEST_CASE() 371 BOOST_REQUIRE_EQUAL(16, (int)lookup->template_length); in BOOST_AUTO_TEST_CASE() 417 BOOST_REQUIRE_EQUAL(16, (int)lookup->template_length); in BOOST_AUTO_TEST_CASE() 463 BOOST_REQUIRE_EQUAL(16, (int)lookup->template_length); in BOOST_AUTO_TEST_CASE()
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/dports/biology/ncbi-toolkit/ncbi/algo/blast/api/ |
H A D | blast_options_api.h | 105 Int2 SBlastOptionsSetDiscMbParams(SBlastOptions* options, Int4 template_length,
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H A D | blast_options_api.c | 197 Int2 SBlastOptionsSetDiscMbParams(SBlastOptions* options, Int4 template_length, in SBlastOptionsSetDiscMbParams() argument 204 options->lookup_options->mb_template_length = template_length; in SBlastOptionsSetDiscMbParams()
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/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/app/magicblast/ |
H A D | magicblast_util.cpp | 1004 int template_length = 0; in PrintSAM() local 1011 template_length = (int)mate_range.GetTo() - (int)range.GetFrom() + 1; in PrintSAM() 1014 template_length = in PrintSAM() 1068 && template_length < kMaxInsertSize) { in PrintSAM() 1075 && abs(template_length) < kMaxInsertSize) { in PrintSAM() 1306 ostr << template_length; in PrintSAM()
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/dports/biology/ncbi-toolkit/ncbi/algo/blast/core/ |
H A D | blast_nascan.c | 2213 Int4 template_length = mb_lt->template_length; in s_MB_DiscWordScanSubject_1() local 2220 while(index < scan_range[0] + template_length) { in s_MB_DiscWordScanSubject_1() 2228 switch (index - (scan_range[0] + template_length)) { in s_MB_DiscWordScanSubject_1() 2302 Int4 template_length = mb_lt->template_length; in s_MB_DiscWordScanSubject_TwoTemplates_1() local 2309 while(index < scan_range[0] + template_length) { in s_MB_DiscWordScanSubject_TwoTemplates_1() 2317 switch (index - (scan_range[0] + template_length)) { in s_MB_DiscWordScanSubject_TwoTemplates_1() 2397 ASSERT(mb_lt->template_length == 18); in s_MB_DiscWordScanSubject_11_18_1() 2510 ASSERT(mb_lt->template_length == 21); in s_MB_DiscWordScanSubject_11_21_1()
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H A D | blast_nalookup.c | 670 Int4 template_length; in s_FillDiscMBTable() local 720 mb_lt->template_length = lookup_options->mb_template_length; in s_FillDiscMBTable() 721 template_length = lookup_options->mb_template_length; in s_FillDiscMBTable() 741 from = loc->ssr->left - (template_length - 2); in s_FillDiscMBTable() 742 to = loc->ssr->right - (template_length - 2); in s_FillDiscMBTable() 744 pos = seq + template_length; in s_FillDiscMBTable() 752 pos = seq + template_length; in s_FillDiscMBTable()
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/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/algo/blast/core/ |
H A D | blast_nascan.c | 2213 Int4 template_length = mb_lt->template_length; in s_MB_DiscWordScanSubject_1() local 2220 while(index < scan_range[0] + template_length) { in s_MB_DiscWordScanSubject_1() 2228 switch (index - (scan_range[0] + template_length)) { in s_MB_DiscWordScanSubject_1() 2302 Int4 template_length = mb_lt->template_length; in s_MB_DiscWordScanSubject_TwoTemplates_1() local 2309 while(index < scan_range[0] + template_length) { in s_MB_DiscWordScanSubject_TwoTemplates_1() 2317 switch (index - (scan_range[0] + template_length)) { in s_MB_DiscWordScanSubject_TwoTemplates_1() 2397 ASSERT(mb_lt->template_length == 18); in s_MB_DiscWordScanSubject_11_18_1() 2510 ASSERT(mb_lt->template_length == 21); in s_MB_DiscWordScanSubject_11_21_1()
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H A D | blast_nalookup.c | 670 Int4 template_length; in s_FillDiscMBTable() local 720 mb_lt->template_length = lookup_options->mb_template_length; in s_FillDiscMBTable() 721 template_length = lookup_options->mb_template_length; in s_FillDiscMBTable() 741 from = loc->ssr->left - (template_length - 2); in s_FillDiscMBTable() 742 to = loc->ssr->right - (template_length - 2); in s_FillDiscMBTable() 744 pos = seq + template_length; in s_FillDiscMBTable() 752 pos = seq + template_length; in s_FillDiscMBTable()
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/dports/biology/ncbi-blast+/ncbi-blast-2.12.0+-src/c++/src/algo/blast/core/ |
H A D | blast_nascan.c | 2213 Int4 template_length = mb_lt->template_length; in s_MB_DiscWordScanSubject_1() local 2220 while(index < scan_range[0] + template_length) { in s_MB_DiscWordScanSubject_1() 2228 switch (index - (scan_range[0] + template_length)) { in s_MB_DiscWordScanSubject_1() 2302 Int4 template_length = mb_lt->template_length; in s_MB_DiscWordScanSubject_TwoTemplates_1() local 2309 while(index < scan_range[0] + template_length) { in s_MB_DiscWordScanSubject_TwoTemplates_1() 2317 switch (index - (scan_range[0] + template_length)) { in s_MB_DiscWordScanSubject_TwoTemplates_1() 2397 ASSERT(mb_lt->template_length == 18); in s_MB_DiscWordScanSubject_11_18_1() 2510 ASSERT(mb_lt->template_length == 21); in s_MB_DiscWordScanSubject_11_21_1()
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H A D | blast_nalookup.c | 670 Int4 template_length; in s_FillDiscMBTable() local 720 mb_lt->template_length = lookup_options->mb_template_length; in s_FillDiscMBTable() 721 template_length = lookup_options->mb_template_length; in s_FillDiscMBTable() 741 from = loc->ssr->left - (template_length - 2); in s_FillDiscMBTable() 742 to = loc->ssr->right - (template_length - 2); in s_FillDiscMBTable() 744 pos = seq + template_length; in s_FillDiscMBTable() 752 pos = seq + template_length; in s_FillDiscMBTable()
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/dports/biology/ncbi-toolkit/ncbi/tools/ |
H A D | lookup.c | 926 Int2 template_length; in MegaBlastBuildLookupTable() local 954 template_length = mb_params->template_length; in MegaBlastBuildLookupTable() 955 extra_length = template_length - word_length; in MegaBlastBuildLookupTable()
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