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Searched refs:template_length (Results 1 – 25 of 53) sorted by relevance

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/dports/biology/py-crossmap/CrossMap-0.5.4/lib/cmmodule/
H A Dmapbam.py193 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 …]
/dports/biology/hhsuite/hh-suite-3.3.0/scripts/
H A Dhh_reader.py45 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,
/dports/devel/gnulib/gnulib-20140202-stable/build-aux/
H A Dmktempd118 template_length=`echo "$template" | wc -c`
120 nx=`expr $template_length - $nx`
/dports/security/pkcs11-tools/pkcs11-tools-2.5.0/.gnulib/build-aux/
H A Dmktempd118 template_length=`echo "$template" | wc -c`
120 nx=`expr $template_length - $nx`
/dports/audio/gsequencer/gsequencer-3.10.4/ags/audio/fx/
H A Dags_fx_pattern_audio_signal.c164 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()
/dports/biology/py-deeptools/deepTools-3.5.1/deeptools/
H A DgetFragmentAndReadSize.py41 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))
H A Dutilities.py56 if abs(read.template_length) > 0:
58 return read.template_length
59 return abs(read.template_length)
H A DcorrectGCBias.py138 fragStart = read.reference_end + read.template_length
139 elif read.template_length >= read.query_alignment_length:
141 fragEnd = read.pos + read.template_length
H A DalignmentSieve.py190 b2.template_length = tLen - deltaTLen
192 b2.template_length = tLen + deltaTLen
/dports/biology/py-biopython/biopython-1.79/Bio/Blast/
H A DNCBIWWW.py81 template_length=None,
190 ("TEMPLATE_LENGTH", template_length),
/dports/science/apbs/apbs-pdb2pqr-apbs-1.5-102-g500c1473/pdb2pqr/propka30/Source/
H A Dmutate.py1054 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))
/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/algo/blast/unit_tests/api/
H A Dntscan_unit_test.cpp413 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()
H A Dntlookup_unit_test.cpp279 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()
/dports/biology/ncbi-blast+/ncbi-blast-2.12.0+-src/c++/src/algo/blast/unit_tests/api/
H A Dntscan_unit_test.cpp413 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()
H A Dntlookup_unit_test.cpp279 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()
/dports/biology/ncbi-toolkit/ncbi/algo/blast/api/
H A Dblast_options_api.h105 Int2 SBlastOptionsSetDiscMbParams(SBlastOptions* options, Int4 template_length,
H A Dblast_options_api.c197 Int2 SBlastOptionsSetDiscMbParams(SBlastOptions* options, Int4 template_length, in SBlastOptionsSetDiscMbParams() argument
204 options->lookup_options->mb_template_length = template_length; in SBlastOptionsSetDiscMbParams()
/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/app/magicblast/
H A Dmagicblast_util.cpp1004 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()
/dports/biology/ncbi-toolkit/ncbi/algo/blast/core/
H A Dblast_nascan.c2213 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()
H A Dblast_nalookup.c670 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()
/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/algo/blast/core/
H A Dblast_nascan.c2213 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()
H A Dblast_nalookup.c670 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()
/dports/biology/ncbi-blast+/ncbi-blast-2.12.0+-src/c++/src/algo/blast/core/
H A Dblast_nascan.c2213 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()
H A Dblast_nalookup.c670 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()
/dports/biology/ncbi-toolkit/ncbi/tools/
H A Dlookup.c926 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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