| /dports/biology/bedtools/bedtools2-2.30.0/test/flank/ |
| H A D | test-flank.sh | 31 $BT flank -i a.bed -b 5 -g tiny.genome > obs
44 $BT flank -i a.bed -l 5 -r 5 -g tiny.genome > obs
55 $BT flank -i a.bed -l 5 -r 0 -g tiny.genome > obs
66 $BT flank -i a.bed -l 0 -r 5 -g tiny.genome > obs
77 $BT flank -i a.bed -l 5 -r 0 -s -g tiny.genome > obs
88 $BT flank -i a.bed -l 0 -r 5 -s -g tiny.genome > obs
101 $BT flank -i a.bed -b 5 -s -g tiny.genome > obs
114 $BT flank -i a.bed -b 200 -g tiny.genome > obs
125 $BT flank -i a.bed -l 0 -r 1000 -g tiny.genome > obs
138 $BT flank -i a.bed -b 2000 -g tiny.genome > obs
[all …]
|
| /dports/biology/bedtools/bedtools2-2.30.0/docs/content/tools/ |
| H A D | flank.rst | 4 *flank*
9 .. image:: ../images/tool-glyphs/flank-glyph.png
14 ``bedtools flank`` will create two new flanking intervals for each interval in
15 a BED/GFF/VCF file. Note that ``flank`` will restrict the created flanking
22 ``bedtools flank`` requires a *genome* file defining the length of each
35 bedtools flank [OPTIONS] -i <BED/GFF/VCF> -g <GENOME> [-b or (-l and -r)]
71 $ bedtools flank -i A.bed -g my.genome -b 5
77 $ bedtools flank -i A.bed -g my.genome -l 2 -r 3
87 chromosome, ``bedtools flank`` will "clip" the feature accordingly.
98 $ bedtools flank -i A.bed -g my.genome -b 800
[all …]
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| /dports/devel/mongo-c-driver/mongo-c-driver-1.8.1/tests/binary/ |
| H A D | gridfs-large.dat | 5 …af, corned beef flank sausage shank turkey kielbasa kevin. Shoulder shankle salami, filet mignon b…
14 …af, corned beef flank sausage shank turkey kielbasa kevin. Shoulder shankle salami, filet mignon b…
23 …af, corned beef flank sausage shank turkey kielbasa kevin. Shoulder shankle salami, filet mignon b…
32 …af, corned beef flank sausage shank turkey kielbasa kevin. Shoulder shankle salami, filet mignon b…
41 …af, corned beef flank sausage shank turkey kielbasa kevin. Shoulder shankle salami, filet mignon b…
50 …af, corned beef flank sausage shank turkey kielbasa kevin. Shoulder shankle salami, filet mignon b…
59 …af, corned beef flank sausage shank turkey kielbasa kevin. Shoulder shankle salami, filet mignon b…
68 …af, corned beef flank sausage shank turkey kielbasa kevin. Shoulder shankle salami, filet mignon b…
77 …af, corned beef flank sausage shank turkey kielbasa kevin. Shoulder shankle salami, filet mignon b…
86 …af, corned beef flank sausage shank turkey kielbasa kevin. Shoulder shankle salami, filet mignon b…
[all …]
|
| H A D | gridfs.dat | 1 …n pastrami frankfurter jowl. Short ribs ball tip rump doner t-bone. Shank flank short loin biltong…
3 …derloin rump shoulder jowl shank beef. Hamburger pork loin pancetta jowl sausage, short ribs flank.
5 …af, corned beef flank sausage shank turkey kielbasa kevin. Shoulder shankle salami, filet mignon b…
7 …flank, strip steak t-bone sausage capicola pork loin frankfurter corned beef. Doner pork drumstick…
|
| /dports/misc/thrill/thrill-12c5b59bca66df93b66628b3829027bd0f110dd9/tests/inputs/ |
| H A D | wordcount.in | 1 …n kevin landjaeger capicola venison rump doner salami filet mignon boudin flank fatback frankfurte…
3 …douille flank alcatra brisket kevin tongue landjaeger flank leberkas brisket beef ribs salami bilt…
7 …usage pancetta tri-tip shank swine bacon boudin prosciutto swine rump ham flank pancetta meatloaf …
11 …n kevin landjaeger capicola venison rump doner salami filet mignon boudin flank fatback frankfurte…
13 …douille flank alcatra brisket kevin tongue landjaeger flank leberkas brisket beef ribs salami bilt…
17 …usage pancetta tri-tip shank swine bacon boudin prosciutto swine rump ham flank pancetta meatloaf …
21 …n kevin landjaeger capicola venison rump doner salami filet mignon boudin flank fatback frankfurte…
23 …douille flank alcatra brisket kevin tongue landjaeger flank leberkas brisket beef ribs salami bilt…
27 …usage pancetta tri-tip shank swine bacon boudin prosciutto swine rump ham flank pancetta meatloaf …
31 …n kevin landjaeger capicola venison rump doner salami filet mignon boudin flank fatback frankfurte…
[all …]
|
| /dports/biology/p5-Bio-Variation/Bio-Variation-1.7.5/bin/ |
| H A D | bp_flanks | 24 my $flank = 100; # flank length on both sides of the region
31 GetOptions ("help" => \$help, "flanklength=i" => \$flank,
47 &extract($seq, \@pos, $flank);
86 my ($seq, $pos, $flank) = @_;
135 my $five_start = $start - $flank;
138 my $three_end = $start + $allele_len + $flank;
139 $three_end = $seq->length if $start + $allele_len + $flank > $seq->length;
|
| /dports/biology/abyss/abyss-2.3.1/DAssembler/ |
| H A D | DAssembler.cpp | 506 string flank = contig.substr(contig.size()-opt::read_length); in main() local
510 read_list.begin(), read_list.end(), flank); in main()
518 if (flank != flank_read.seq){ in main()
521 flank_read = RotatedRead(flank, 1); in main()
|
| /dports/emulators/mess/mame-mame0226/src/mame/drivers/ |
| H A D | alfaskop41xx.cpp | 136 bool flank = false; member in alfaskop4110_state
495 if (flank) in device_timer()
515 m_tia_adlc->rxc_w(flank ? 1 : 0); in device_timer()
518 flank = !flank; in device_timer()
|
| /dports/emulators/mame/mame-mame0226/src/mame/drivers/ |
| H A D | alfaskop41xx.cpp | 136 bool flank = false; member in alfaskop4110_state
495 if (flank) in device_timer()
515 m_tia_adlc->rxc_w(flank ? 1 : 0); in device_timer()
518 flank = !flank; in device_timer()
|
| /dports/biology/bedtools/bedtools2-2.30.0/tutorial/ |
| H A D | answers.md | 103 …r last exon). (Hint - have a look at the [flank](http://bedtools.readthedocs.org/en/latest/content…
107 bedtools flank -l 2 -r 2 -i exons.bed -g genome.txt > splice-sites.bed
|
| /dports/games/pcgen/pcgen/data/modern/rpg_objects/blood_and_blades/ |
| H A D | bloodandblades_abilities.lst | 4 … any time your target would be denied a Dexterity bonus to AC or when you flank your target|SneakA…
|
| /dports/devel/py-ramlfications/ramlfications-0.1.9/tests/data/examples/includes/ |
| H A D | example.md | 7 …wl doner andouille cupim meatball. Porchetta hamburger filet mignon jerky flank, meatball salami b…
|
| /dports/textproc/py-html2text/html2text-2020.1.16/test/ |
| H A D | emdash-para.md | 2 exercitation flank quis veniam officia. Chuck dolor esse, occaecat est elit
|
| /dports/textproc/py-html2text2018/html2text-2018.1.9/test/ |
| H A D | emdash-para.md | 2 exercitation flank quis veniam officia. Chuck dolor esse, occaecat est elit
|
| /dports/biology/bedtools/bedtools2-2.30.0/docs/content/ |
| H A D | bedtools-suite.rst | 30 tools/flank
|
| /dports/biology/abyss/abyss-2.3.1/Sealer/ |
| H A D | README.md | 99 …l start position of gap on scaffold]\_[size of gap]/[1 or 2 indicating whether left or right flank]
128 * `--print-flanks`: outputs flank files
130 * `-L`,`--flank-length=N`: length of flanks to be used as pseudoreads [`100`]
147 * `-m,`--flank-mismatches=N`: max mismatches between paths and flanks; use 'nolimit' for no limit […
|
| /dports/biology/p5-BioPerl/BioPerl-1.7.7/t/data/ |
| H A D | BEL16-LTR_AG.embl | 28 CC BEL16-LTR_AG flank an internal portion of BEL16_AG (deposited as
|
| /dports/biology/vcflib/vcflib-1.0.2/doc/ |
| H A D | vcfprimers.md | 27 experiments. Primers extracted which would flank all of the alleles at multi-allelic
|
| /dports/biology/minimap2/minimap2-2.24/ |
| H A D | cookbook.md | 112 minimap2 -ax splice --splice-flank=no SIRV_E2.fa SIRV_ont-cdna.fa | paftools.js junceval SIRV_E2C.g…
116 `--splice-flank=no` asks minimap2 no to model this additional base.
130 `--splice-flank=no` helps junction accuracy for SIRV data.
139 error. Applying `--splice-flank=no` fixes this alignment error.
|
| /dports/games/tanks-of-freedom/Tanks-of-Freedom-0.7.0-beta/translations/campaigns/ |
| H A D | campaign_ja.csv | 74 MISSION_5_FLANK,"With the right flank secured, we were able to bring in some reinforcements."
87 MISSION_6_APP_TOWERS_1,"There are two comm towers on the left flank."
101 MISSION_7_LEFT_CLAIMED,"Left flank secure."
102 MISSION_7_RIGHT_CLAIMED,"Right flank secure."
161 MISSION_12_CROSSROAD_2,"The enemy base is going to put a pressure on us from the flank. Take it out…
|
| H A D | campaign_ru.csv | 74 MISSION_5_FLANK,"With the right flank secured, we were able to bring in some reinforcements."
87 MISSION_6_APP_TOWERS_1,"There are two comm towers on the left flank."
101 MISSION_7_LEFT_CLAIMED,"Left flank secure."
102 MISSION_7_RIGHT_CLAIMED,"Right flank secure."
161 MISSION_12_CROSSROAD_2,"The enemy base is going to put a pressure on us from the flank. Take it out…
|
| /dports/cad/qelectrotech/qet-0.7.0/elements/20_logic/30_ladder/11_inputs/ |
| H A D | entree_fn.elmt | 15 <name lang="nl">Ingang (neergaande flank)</name>
|
| H A D | entree_fp.elmt | 15 <name lang="nl">Ingang (Opgaande flank)</name>
|
| /dports/biology/gatk/gatk-4.2.0.0/src/main/java/org/broadinstitute/hellbender/tools/walkers/haplotypecaller/ |
| H A D | HaplotypeCallerEngine.java | 713 …ingResult.nonVariantLeftFlankRegion().ifPresent(flank -> result.addAll(referenceModelForNoVariatio… in callRegion()
720 …ngResult.nonVariantRightFlankRegion().ifPresent(flank -> result.addAll(referenceModelForNoVariatio… in callRegion()
|
| /dports/biology/gatk/gatk-4.2.0.0/src/main/java/org/broadinstitute/hellbender/tools/walkers/mutect/ |
| H A D | Mutect2Engine.java | 270 …ingResult.nonVariantLeftFlankRegion().ifPresent(flank -> result.addAll(referenceModelForNoVariatio… in callRegion()
276 …ngResult.nonVariantRightFlankRegion().ifPresent(flank -> result.addAll(referenceModelForNoVariatio… in callRegion()
|