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/dports/biology/p5-transdecoder/TransDecoder-TransDecoder-v5.4.0/PerlLib/
H A DGTF.pm132 return $gtf;
140 my ($gtf) = @_;
164 my ($gtf) = @_;
165 $gtf->_update;
170 my ($gtf) = @_;
171 $gtf->_update;
330 $gtf->_update;
409 $gtf->_update;
441 $gtf->_update;
470 $gtf->_update;
[all …]
/dports/science/py-dipy/dipy-1.4.1/dipy/reconst/tests/
H A Dtest_fwdti.py61 gtf = GTF[0, i, j]
64 fractions=[(1-gtf) * 100, gtf*100], snr=None)
80 fractions=[(1-gtf) * 100, gtf*100], snr=None)
99 assert_almost_equal(Ffwe, gtf)
110 assert_almost_equal(Ffwe, gtf)
120 fractions=[(1-gtf) * 100, gtf*100], snr=None)
162 fractions=[(1-gtf) * 100, gtf*100], snr=None)
223 fractions=[(1-gtf) * 100, gtf*100], snr=None)
283 fractions=[(1-gtf) * 100, gtf*100], snr=None)
305 gtf = 0.55
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/dports/multimedia/v4l_compat/v4l-utils-4l-utils-1.20.0/utils/v4l2-ctl/
H A Dv4l2-ctl-modes.cpp423 if (!gtf) { in calc_gtf_modeline()
505 gtf->width = h_pixel; in calc_gtf_modeline()
506 gtf->hfrontporch = h_fp; in calc_gtf_modeline()
507 gtf->hsync = h_sync; in calc_gtf_modeline()
508 gtf->hbackporch = h_bp; in calc_gtf_modeline()
510 gtf->height = v_lines; in calc_gtf_modeline()
511 gtf->vfrontporch = v_fp; in calc_gtf_modeline()
512 gtf->vsync = v_sync; in calc_gtf_modeline()
513 gtf->vbackporch = v_bp; in calc_gtf_modeline()
521 gtf->il_vsync = v_sync; in calc_gtf_modeline()
[all …]
/dports/multimedia/libv4l/v4l-utils-4l-utils-1.20.0/utils/v4l2-ctl/
H A Dv4l2-ctl-modes.cpp423 if (!gtf) { in calc_gtf_modeline()
505 gtf->width = h_pixel; in calc_gtf_modeline()
506 gtf->hfrontporch = h_fp; in calc_gtf_modeline()
507 gtf->hsync = h_sync; in calc_gtf_modeline()
508 gtf->hbackporch = h_bp; in calc_gtf_modeline()
510 gtf->height = v_lines; in calc_gtf_modeline()
511 gtf->vfrontporch = v_fp; in calc_gtf_modeline()
512 gtf->vsync = v_sync; in calc_gtf_modeline()
513 gtf->vbackporch = v_bp; in calc_gtf_modeline()
521 gtf->il_vsync = v_sync; in calc_gtf_modeline()
[all …]
/dports/multimedia/v4l-utils/v4l-utils-4l-utils-1.20.0/utils/v4l2-ctl/
H A Dv4l2-ctl-modes.cpp423 if (!gtf) { in calc_gtf_modeline()
505 gtf->width = h_pixel; in calc_gtf_modeline()
506 gtf->hfrontporch = h_fp; in calc_gtf_modeline()
507 gtf->hsync = h_sync; in calc_gtf_modeline()
508 gtf->hbackporch = h_bp; in calc_gtf_modeline()
510 gtf->height = v_lines; in calc_gtf_modeline()
511 gtf->vfrontporch = v_fp; in calc_gtf_modeline()
512 gtf->vsync = v_sync; in calc_gtf_modeline()
513 gtf->vbackporch = v_bp; in calc_gtf_modeline()
521 gtf->il_vsync = v_sync; in calc_gtf_modeline()
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/dports/biology/py-deeptoolsintervals/deeptoolsintervals-0.1.9/
H A DREADME.md20 >>> gtf = GTF("some_file.gtf")
25 >>> gtf = GTF(["some_file.gtf", "some_other_file.bed.gz"])
32 >>> gtf = GTF(["some_file.gtf", "some_other_file.bed.gz"], keepExons=True)
67 >>> gtf = GTF(["some_file.gtf", "some_other_file.bed.gz", "some_file.gtf"], keepExons=True)
89 >>> gtf = GTF("foo.gtf", keepExons=True)
96 >>> gtf = GTF("foo.gtf")
103 >>> gtf = GTF("foo.gtf")
113 >>> gtf = Enrichment(["foo.gtf", "bar.bed"])
118 >>> gtf = Enrichment(["foo.gtf", "bar.bed"], labels=["this will be ignored", "peaks"])
134 >>> gtf = Enrichment("GRCh38.84.gtf.gz")
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/dports/net/tigervnc-server/tigervnc-1.12.0/unix/xserver/hw/xfree86/utils/gtf/
H A DMakefile.in137 am_gtf_OBJECTS = gtf-gtf.$(OBJEXT)
162 am__depfiles_remade = ./$(DEPDIR)/gtf-gtf.Po
569 gtf_SOURCES = gtf.c
656 @rm -f gtf$(EXEEXT)
694 gtf-gtf.o: gtf.c
695 …gtf_CFLAGS) $(CFLAGS) -MT gtf-gtf.o -MD -MP -MF $(DEPDIR)/gtf-gtf.Tpo -c -o gtf-gtf.o `test -f 'gt…
696 @am__fastdepCC_TRUE@ $(AM_V_at)$(am__mv) $(DEPDIR)/gtf-gtf.Tpo $(DEPDIR)/gtf-gtf.Po
701 gtf-gtf.obj: gtf.c
703 @am__fastdepCC_TRUE@ $(AM_V_at)$(am__mv) $(DEPDIR)/gtf-gtf.Tpo $(DEPDIR)/gtf-gtf.Po
841 -rm -f ./$(DEPDIR)/gtf-gtf.Po
[all …]
/dports/x11-servers/xorg-dmx/xorg-server-1.20.13/hw/xfree86/utils/gtf/
H A DMakefile.in137 am_gtf_OBJECTS = gtf-gtf.$(OBJEXT)
162 am__depfiles_remade = ./$(DEPDIR)/gtf-gtf.Po
569 gtf_SOURCES = gtf.c
656 @rm -f gtf$(EXEEXT)
694 gtf-gtf.o: gtf.c
695 …gtf_CFLAGS) $(CFLAGS) -MT gtf-gtf.o -MD -MP -MF $(DEPDIR)/gtf-gtf.Tpo -c -o gtf-gtf.o `test -f 'gt…
696 @am__fastdepCC_TRUE@ $(AM_V_at)$(am__mv) $(DEPDIR)/gtf-gtf.Tpo $(DEPDIR)/gtf-gtf.Po
701 gtf-gtf.obj: gtf.c
703 @am__fastdepCC_TRUE@ $(AM_V_at)$(am__mv) $(DEPDIR)/gtf-gtf.Tpo $(DEPDIR)/gtf-gtf.Po
841 -rm -f ./$(DEPDIR)/gtf-gtf.Po
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/dports/x11-servers/xorg-vfbserver/xorg-server-1.20.13/hw/xfree86/utils/gtf/
H A DMakefile.in137 am_gtf_OBJECTS = gtf-gtf.$(OBJEXT)
162 am__depfiles_remade = ./$(DEPDIR)/gtf-gtf.Po
569 gtf_SOURCES = gtf.c
656 @rm -f gtf$(EXEEXT)
694 gtf-gtf.o: gtf.c
695 …gtf_CFLAGS) $(CFLAGS) -MT gtf-gtf.o -MD -MP -MF $(DEPDIR)/gtf-gtf.Tpo -c -o gtf-gtf.o `test -f 'gt…
696 @am__fastdepCC_TRUE@ $(AM_V_at)$(am__mv) $(DEPDIR)/gtf-gtf.Tpo $(DEPDIR)/gtf-gtf.Po
701 gtf-gtf.obj: gtf.c
703 @am__fastdepCC_TRUE@ $(AM_V_at)$(am__mv) $(DEPDIR)/gtf-gtf.Tpo $(DEPDIR)/gtf-gtf.Po
841 -rm -f ./$(DEPDIR)/gtf-gtf.Po
[all …]
/dports/x11-servers/xwayland/xorg-server-1.20.13/hw/xfree86/utils/gtf/
H A DMakefile.in137 am_gtf_OBJECTS = gtf-gtf.$(OBJEXT)
162 am__depfiles_remade = ./$(DEPDIR)/gtf-gtf.Po
569 gtf_SOURCES = gtf.c
656 @rm -f gtf$(EXEEXT)
694 gtf-gtf.o: gtf.c
695 …gtf_CFLAGS) $(CFLAGS) -MT gtf-gtf.o -MD -MP -MF $(DEPDIR)/gtf-gtf.Tpo -c -o gtf-gtf.o `test -f 'gt…
696 @am__fastdepCC_TRUE@ $(AM_V_at)$(am__mv) $(DEPDIR)/gtf-gtf.Tpo $(DEPDIR)/gtf-gtf.Po
701 gtf-gtf.obj: gtf.c
703 @am__fastdepCC_TRUE@ $(AM_V_at)$(am__mv) $(DEPDIR)/gtf-gtf.Tpo $(DEPDIR)/gtf-gtf.Po
841 -rm -f ./$(DEPDIR)/gtf-gtf.Po
[all …]
/dports/x11-servers/xorg-server/xorg-server-1.20.13/hw/xfree86/utils/gtf/
H A DMakefile.in137 am_gtf_OBJECTS = gtf-gtf.$(OBJEXT)
162 am__depfiles_remade = ./$(DEPDIR)/gtf-gtf.Po
569 gtf_SOURCES = gtf.c
656 @rm -f gtf$(EXEEXT)
694 gtf-gtf.o: gtf.c
695 …gtf_CFLAGS) $(CFLAGS) -MT gtf-gtf.o -MD -MP -MF $(DEPDIR)/gtf-gtf.Tpo -c -o gtf-gtf.o `test -f 'gt…
696 @am__fastdepCC_TRUE@ $(AM_V_at)$(am__mv) $(DEPDIR)/gtf-gtf.Tpo $(DEPDIR)/gtf-gtf.Po
701 gtf-gtf.obj: gtf.c
703 @am__fastdepCC_TRUE@ $(AM_V_at)$(am__mv) $(DEPDIR)/gtf-gtf.Tpo $(DEPDIR)/gtf-gtf.Po
841 -rm -f ./$(DEPDIR)/gtf-gtf.Po
[all …]
H A DMakefile.in.bak137 am_gtf_OBJECTS = gtf-gtf.$(OBJEXT)
162 am__depfiles_remade = ./$(DEPDIR)/gtf-gtf.Po
694 gtf-gtf.o: gtf.c
695 …gtf_CFLAGS) $(CFLAGS) -MT gtf-gtf.o -MD -MP -MF $(DEPDIR)/gtf-gtf.Tpo -c -o gtf-gtf.o `test -f 'gt…
696 @am__fastdepCC_TRUE@ $(AM_V_at)$(am__mv) $(DEPDIR)/gtf-gtf.Tpo $(DEPDIR)/gtf-gtf.Po
697 @AMDEP_TRUE@@am__fastdepCC_FALSE@ $(AM_V_CC)source='gtf.c' object='gtf-gtf.o' libtool=no @AMDEPBACK…
701 gtf-gtf.obj: gtf.c
702 …-MT gtf-gtf.obj -MD -MP -MF $(DEPDIR)/gtf-gtf.Tpo -c -o gtf-gtf.obj `if test -f 'gtf.c'; then $(CY…
703 @am__fastdepCC_TRUE@ $(AM_V_at)$(am__mv) $(DEPDIR)/gtf-gtf.Tpo $(DEPDIR)/gtf-gtf.Po
841 -rm -f ./$(DEPDIR)/gtf-gtf.Po
[all …]
/dports/x11-servers/xephyr/xorg-server-1.20.13/hw/xfree86/utils/gtf/
H A DMakefile.in137 am_gtf_OBJECTS = gtf-gtf.$(OBJEXT)
162 am__depfiles_remade = ./$(DEPDIR)/gtf-gtf.Po
569 gtf_SOURCES = gtf.c
656 @rm -f gtf$(EXEEXT)
694 gtf-gtf.o: gtf.c
695 …gtf_CFLAGS) $(CFLAGS) -MT gtf-gtf.o -MD -MP -MF $(DEPDIR)/gtf-gtf.Tpo -c -o gtf-gtf.o `test -f 'gt…
696 @am__fastdepCC_TRUE@ $(AM_V_at)$(am__mv) $(DEPDIR)/gtf-gtf.Tpo $(DEPDIR)/gtf-gtf.Po
701 gtf-gtf.obj: gtf.c
703 @am__fastdepCC_TRUE@ $(AM_V_at)$(am__mv) $(DEPDIR)/gtf-gtf.Tpo $(DEPDIR)/gtf-gtf.Po
841 -rm -f ./$(DEPDIR)/gtf-gtf.Po
[all …]
/dports/x11-servers/xorg-nestserver/xorg-server-1.20.13/hw/xfree86/utils/gtf/
H A DMakefile.in137 am_gtf_OBJECTS = gtf-gtf.$(OBJEXT)
162 am__depfiles_remade = ./$(DEPDIR)/gtf-gtf.Po
569 gtf_SOURCES = gtf.c
656 @rm -f gtf$(EXEEXT)
694 gtf-gtf.o: gtf.c
695 …gtf_CFLAGS) $(CFLAGS) -MT gtf-gtf.o -MD -MP -MF $(DEPDIR)/gtf-gtf.Tpo -c -o gtf-gtf.o `test -f 'gt…
696 @am__fastdepCC_TRUE@ $(AM_V_at)$(am__mv) $(DEPDIR)/gtf-gtf.Tpo $(DEPDIR)/gtf-gtf.Po
701 gtf-gtf.obj: gtf.c
703 @am__fastdepCC_TRUE@ $(AM_V_at)$(am__mv) $(DEPDIR)/gtf-gtf.Tpo $(DEPDIR)/gtf-gtf.Po
841 -rm -f ./$(DEPDIR)/gtf-gtf.Po
[all …]
/dports/www/chromium-legacy/chromium-88.0.4324.182/third_party/angle/third_party/VK-GL-CTS/src/external/openglcts/modules/
H A DglcTestPackageRegistry.cpp104 return new gtf::es2::TestPackage(testCtx, "GTF-GLES2"); in createES2GTFPackage()
123 return new gtf::es3::TestPackage(testCtx, "GTF-GLES3"); in createES30GTFPackage()
221 return new gtf::gl30::TestPackage(testCtx, "GTF-GL30"); in createGL30GTFPackage()
225 return new gtf::gl31::TestPackage(testCtx, "GTF-GL31"); in createGL31GTFPackage()
229 return new gtf::gl32::TestPackage(testCtx, "GTF-GL32"); in createGL32GTFPackage()
233 return new gtf::gl32::TestPackage(testCtx, "GTF-GL33"); in createGL33GTFPackage()
238 return new gtf::gl40::TestPackage(testCtx, "GTF-GL40"); in createGL40GTFPackage()
242 return new gtf::gl41::TestPackage(testCtx, "GTF-GL41"); in createGL41GTFPackage()
246 return new gtf::gl42::TestPackage(testCtx, "GTF-GL42"); in createGL42GTFPackage()
250 return new gtf::gl43::TestPackage(testCtx, "GTF-GL43"); in createGL43GTFPackage()
[all …]
/dports/multimedia/v4l-utils/linux-5.13-rc2/drivers/ata/
H A Dlibata-acpi.c465 if (gtf) { in ata_dev_get_GTF()
469 __func__, *gtf, rc); in ata_dev_get_GTF()
557 tf->feature = gtf->tf[0]; /* 0x1f1 */ in ata_acpi_gtf_to_tf()
558 tf->nsect = gtf->tf[1]; /* 0x1f2 */ in ata_acpi_gtf_to_tf()
647 const struct ata_acpi_gtf *gtf, in ata_acpi_run_tf() argument
658 if ((gtf->tf[0] == 0) && (gtf->tf[1] == 0) && (gtf->tf[2] == 0) in ata_acpi_run_tf()
659 && (gtf->tf[3] == 0) && (gtf->tf[4] == 0) && (gtf->tf[5] == 0) in ata_acpi_run_tf()
660 && (gtf->tf[6] == 0)) in ata_acpi_run_tf()
663 ata_acpi_gtf_to_tf(dev, gtf, &tf); in ata_acpi_run_tf()
733 rc = ata_dev_get_GTF(dev, &gtf); in ata_acpi_exec_tfs()
[all …]
/dports/multimedia/v4l_compat/linux-5.13-rc2/drivers/ata/
H A Dlibata-acpi.c465 if (gtf) { in ata_dev_get_GTF()
469 __func__, *gtf, rc); in ata_dev_get_GTF()
557 tf->feature = gtf->tf[0]; /* 0x1f1 */ in ata_acpi_gtf_to_tf()
558 tf->nsect = gtf->tf[1]; /* 0x1f2 */ in ata_acpi_gtf_to_tf()
647 const struct ata_acpi_gtf *gtf, in ata_acpi_run_tf() argument
658 if ((gtf->tf[0] == 0) && (gtf->tf[1] == 0) && (gtf->tf[2] == 0) in ata_acpi_run_tf()
659 && (gtf->tf[3] == 0) && (gtf->tf[4] == 0) && (gtf->tf[5] == 0) in ata_acpi_run_tf()
660 && (gtf->tf[6] == 0)) in ata_acpi_run_tf()
663 ata_acpi_gtf_to_tf(dev, gtf, &tf); in ata_acpi_run_tf()
733 rc = ata_dev_get_GTF(dev, &gtf); in ata_acpi_exec_tfs()
[all …]
/dports/multimedia/libv4l/linux-5.13-rc2/drivers/ata/
H A Dlibata-acpi.c465 if (gtf) { in ata_dev_get_GTF()
469 __func__, *gtf, rc); in ata_dev_get_GTF()
557 tf->feature = gtf->tf[0]; /* 0x1f1 */ in ata_acpi_gtf_to_tf()
558 tf->nsect = gtf->tf[1]; /* 0x1f2 */ in ata_acpi_gtf_to_tf()
647 const struct ata_acpi_gtf *gtf, in ata_acpi_run_tf() argument
658 if ((gtf->tf[0] == 0) && (gtf->tf[1] == 0) && (gtf->tf[2] == 0) in ata_acpi_run_tf()
659 && (gtf->tf[3] == 0) && (gtf->tf[4] == 0) && (gtf->tf[5] == 0) in ata_acpi_run_tf()
660 && (gtf->tf[6] == 0)) in ata_acpi_run_tf()
663 ata_acpi_gtf_to_tf(dev, gtf, &tf); in ata_acpi_run_tf()
733 rc = ata_dev_get_GTF(dev, &gtf); in ata_acpi_exec_tfs()
[all …]
/dports/biology/star/STAR-2.7.9a/source/
H A DGenome_transformGenome.cpp32 void Genome::transformGenome(GTF *gtf) in transformGenome() argument
101 transformExonLoci(gtf->exonLoci, transformBlocks); in transformGenome()
128 exonLoci1[0]=gtf->exonLoci; in transformGenome()
129 exonLoci1[1]=gtf->exonLoci; in transformGenome()
131 exon[exT] += gtf->transcriptID.size(); in transformGenome()
132 exon[exG] += gtf->geneID.size(); in transformGenome()
135 appendVector(gtf->geneAttr, gtf->geneAttr); in transformGenome()
136 appendVector(gtf->transcriptStrand, gtf->transcriptStrand); in transformGenome()
137 …gtf->geneID = concatenateVectors(appendString(gtf->geneID, "_h1"), appendString(gtf->geneID, "_h2"… in transformGenome()
138 …gtf->transcriptID = concatenateVectors(appendString(gtf->transcriptID, "_h1"), appendString(gtf->t… in transformGenome()
[all …]
/dports/biology/p5-transdecoder/TransDecoder-TransDecoder-v5.4.0/sample_data/cufflinks_example/
H A DrunMe.sh12 if [ ! -e transcripts.gtf ]; then
13 gunzip -c transcripts.gtf.gz > transcripts.gtf
26 ../../util/gtf_to_alignment_gff3.pl transcripts.gtf > transcripts.gff3
29 ../../util/gtf_genome_to_cdna_fasta.pl transcripts.gtf test.genome.fasta > transcripts.fasta
74 ../../util/gtf_to_bed.pl transcripts.gtf > transcripts.bed
/dports/math/octave-forge-ltfat/ltfat/src/modules/libltfat/src/
H A Dgabtight.c13 LTFAT_COMPLEX* gtf = NULL; in LTFAT_NAME() local
28 CHECKMEM( gtf = LTFAT_NAME_COMPLEX(malloc)(L * R)); in LTFAT_NAME()
33 LTFAT_NAME_REAL(gabtight_fac)(gf, L, R, a, M, gtf); in LTFAT_NAME()
34 CHECKSTATUS( LTFAT_NAME(iwfac)(gtf, L, R, a, M, gt)); in LTFAT_NAME()
39 LTFAT_NAME_REAL(gabtightreal_fac)(gf, L, R, a, M, gtf); in LTFAT_NAME()
40 LTFAT_NAME_REAL(iwfacreal)(gtf, L, R, a, M, gt); in LTFAT_NAME()
45 LTFAT_SAFEFREEALL(gtf, gf); in LTFAT_NAME()
/dports/biology/hisat2/hisat2-2.2.1/docs/_pages/
H A Dhowto.md30 $ wget ftp://ftp.ensembl.org/pub/release-84/gtf/homo_sapiens/Homo_sapiens.GRCh38.84.gtf.gz
31 $ gzip -d Homo_sapiens.GRCh38.84.gtf.gz
32 $ mv Homo_sapiens.GRCh38.84.gtf genome.gtf
33 $ hisat2_extract_splice_sites.py genome.gtf > genome.ss
34 $ hisat2_extract_exons.py genome.gtf > genome.exon
/dports/biology/gatk/gatk-4.2.0.0/scripts/funcotator/data_sources/
H A DgetGencode.sh168 ….ac.uk/pub/databases/gencode/Gencode_human/release_${version}/gencode.v${version}.annotation.gtf.gz
173 …encode/Gencode_human/release_${version}/GRCh37_mapping/gencode.v${fileRefVersion}.annotation.gtf.gz
178 gunzip gencode.v${fileRefVersion}.annotation.gtf.gz
183 ….v${fileRefVersion}.annotation.gtf | sed -e '1,5s$^#\([a-z]\)$##\1$' > gencode.v${fileRefVersion}.…
186 rm gencode.v${fileRefVersion}.annotation.gtf
/dports/biology/p5-Bio-FeatureIO/Bio-FeatureIO-1.6.905/lib/Bio/FeatureIO/
H A Dgtf.pm73 package Bio::FeatureIO::gtf;
75 $Bio::FeatureIO::gtf::AUTHORITY = 'cpan:BIOPERLML';
77 $Bio::FeatureIO::gtf::VERSION = '1.6.905';
/dports/biology/cufflinks/cufflinks-2.2.1-89-gdc3b0cb/cufflinks.xcodeproj/
H A Dcole.pbxuser1662 "-G gtf4.gtf",
1671 "-G sample.gtf",
1678 "-M mask.gtf",
1699 "-G small.gtf",
1827 consensus.gtf,
1828 Neu.gtf,
1834 SAA2.exon.gtf,
1837 transcripts.gtf,
1922 y1_short.gtf,
1923 y2_short.gtf,
[all …]

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