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/dports/biology/star/STAR-2.7.9a/source/
H A DGTF_transcriptGeneSJ.cpp37 for (uint64 iex=0; iex<exonN; iex++) { in transcriptGeneSJ() local
38 exgeLoci[GTF_exgeExStart(iex)]=exonLoci[iex][exS]; in transcriptGeneSJ()
39 exgeLoci[GTF_exgeExEnd(iex)]=exonLoci[iex][exE]; in transcriptGeneSJ()
41 exgeLoci[GTF_exgeGeID(iex)]=exonLoci[iex][exG]; in transcriptGeneSJ()
42 exgeLoci[GTF_exgeTrID(iex)]=exonLoci[iex][exT]; in transcriptGeneSJ()
49 for (uint64 iex=0; iex<exonN; iex++) { in transcriptGeneSJ() local
69 for (uint64 iex=0; iex<=exonN; iex++) { in transcriptGeneSJ() local
78 extrLoci[GTF_extrTrID(iex)]=exonLoci[iex][exT]; in transcriptGeneSJ()
81 extrLoci[GTF_extrGeID(iex)]=exonLoci[iex][exG]; in transcriptGeneSJ()
96 for (uint64 iex=0;iex<=exonN; iex++) { in transcriptGeneSJ() local
[all …]
H A DTranscriptome_quantAlign.cpp44 for (uint32 iex=0; iex<aT.nExons; iex++) { in alignToTranscript() local
45 aT.exons[iex][EX_R]=aG.Lread-(aT.exons[iex][EX_R]+aT.exons[iex][EX_L]); in alignToTranscript()
46 aT.exons[iex][EX_G]=trlength-(aT.exons[iex][EX_G]+aT.exons[iex][EX_L]); in alignToTranscript()
48 for (uint32 iex=0; iex<aT.nExons/2; iex++) { in alignToTranscript() local
49 swap(aT.exons[iex][EX_R],aT.exons[aT.nExons-1-iex][EX_R]); in alignToTranscript()
50 swap(aT.exons[iex][EX_G],aT.exons[aT.nExons-1-iex][EX_G]); in alignToTranscript()
51 swap(aT.exons[iex][EX_L],aT.exons[aT.nExons-1-iex][EX_L]); in alignToTranscript()
52 swap(aT.exons[iex][EX_iFrag],aT.exons[aT.nExons-1-iex][EX_iFrag]); in alignToTranscript()
54 for (uint32 iex=0; iex<(aT.nExons-1)/2; iex++) { in alignToTranscript() local
55 swap(aT.canonSJ[iex],aT.canonSJ[aT.nExons-2-iex]); in alignToTranscript()
[all …]
H A DTranscript_alignScore.cpp13 for (uint iex=0;iex<nExons;iex++) { in alignScore() local
14 for (uint ii=0;ii<exons[iex][EX_L];ii++) { in alignScore()
15 char r1=R[ii+exons[iex][EX_R]]; in alignScore()
16 char g1=G[ii+exons[iex][EX_G]]; in alignScore()
27 for (uint iex=0;iex<nExons-1;iex++) {//score junctions in alignScore() local
28 if (sjAnnot[iex]==1) { in alignScore()
31 switch (canonSJ[iex]) { in alignScore()
35 …maxScore += (exons[iex+1][EX_R]-exons[iex][EX_R]-exons[iex][EX_L])*P.scoreInsBase + P.scoreInsOpen; in alignScore()
38 …maxScore += (exons[iex+1][EX_G]-exons[iex][EX_G]-exons[iex][EX_L])*P.scoreDelBase + P.scoreDelOpen; in alignScore()
H A DReadAlign_peOverlapMergeMap.cpp186 for (uint iex=0; iex<t.nExons; iex++) {//cycle through the exons in peOverlapSEtoPE() local
187 …if (t.exons[iex][EX_R] >= mEnd[imate] || t.exons[iex][EX_R]+t.exons[iex][EX_L] <= mSta[imate]) {//… in peOverlapSEtoPE()
193 if (iex<t.nExons-1) { in peOverlapSEtoPE()
196 sjStr[nExons]=t.sjStr[iex]; in peOverlapSEtoPE()
213 exons[nExons][EX_L]-=t.exons[iex][EX_R]+t.exons[iex][EX_L]-mEnd[imate]; in peOverlapSEtoPE()
244 for (uint iex=0;iex<nExons;iex++) {//caclulate total mapped length in peOverlapSEtoPE() local
245 rLength += exons[iex][EX_L]; in peOverlapSEtoPE()
323 for (uint iex=0; iex<tempTrChim[ii].nExons; iex++) { in peOverlapChimericSEtoPE() local
326 segEx[ii]=iex; in peOverlapChimericSEtoPE()
343 for (uint iex=0; iex<tempTrChim[i1].nExons; iex++) { in peOverlapChimericSEtoPE() local
[all …]
H A DstitchWindowAligns.cpp114 for (uint iex=0;iex<trA.nExons-1;iex++) { in stitchWindowAligns() local
140 for (uint iex=0;iex<trA.nExons-1;iex++) { in stitchWindowAligns() local
144 for (uint iex=0;iex<trA.nExons-1;iex++) { in stitchWindowAligns() local
145 if (trA.canonSJ[iex]==0 && trA.sjAnnot[iex]==0) return; in stitchWindowAligns()
156 for (uint iex=0;iex<trA.nExons;iex++) {// in stitchWindowAligns() local
170 for (uint iex=0;iex<trA.nExons-1;iex++) { in stitchWindowAligns() local
171 if (trA.canonSJ[iex]>=0 && trA.sjAnnot[iex]==0) { in stitchWindowAligns()
172 uint jS=trA.exons[iex][EX_G]+trA.exons[iex][EX_L]; in stitchWindowAligns()
182 for (uint iex=0;iex<trA.nExons-1;iex++) {//find the first exon of the second mate in stitchWindowAligns() local
184 iexM2=iex+1; in stitchWindowAligns()
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H A DReadAlign_outputTranscriptSJ.cpp14 for (uint iex=0;iex<trOut.nExons-1;iex++) {//record all junctions in outputTranscriptSJ() local
15 if (trOut.canonSJ[iex]>=0) {//only record junctions, not indels or mate gap in outputTranscriptSJ()
17 … *chunkOutSJ->oneSJ.start=trOut.exons[iex][EX_G]+trOut.exons[iex][EX_L]; //start of the intron in outputTranscriptSJ()
18 *chunkOutSJ->oneSJ.gap=trOut.exons[iex+1][EX_G]-*chunkOutSJ->oneSJ.start; in outputTranscriptSJ()
23 …hunkOutSJ->oneSJ.overhangLeft = min ( (uint32) trOut.exons[iex][EX_L],(uint32) trOut.exons[iex+1][… in outputTranscriptSJ()
42 *chunkOutSJ->oneSJ.motif=trOut.canonSJ[iex]; in outputTranscriptSJ()
43 … *chunkOutSJ->oneSJ.strand=(char) (trOut.canonSJ[iex]==0 ? 0 : (trOut.canonSJ[iex]+1)%2+1); in outputTranscriptSJ()
44 *chunkOutSJ->oneSJ.annot=trOut.sjAnnot[iex]; in outputTranscriptSJ()
/dports/lang/elixir-devel/elixir-1.13.1/lib/elixir/lib/
H A Dinteger.ex27 iex> Integer.is_odd(5)
30 iex> Integer.is_odd(6)
33 iex> Integer.is_odd(-5)
36 iex> Integer.is_odd(0)
52 iex> Integer.is_even(10)
55 iex> Integer.is_even(5)
61 iex> Integer.is_even(0)
78 iex> Integer.pow(2, 0)
80 iex> Integer.pow(2, 1)
89 iex> Integer.pow(3, 4)
[all …]
H A Dbitwise.ex11 iex> use Bitwise
26 iex> 1 &&& 1
34 iex> odd? = fn
38 iex> odd?.(1)
70 iex> bnot(2)
92 iex> ~~~2
131 iex> 9 &&& 3
167 iex> 9 ||| 3
234 iex> 1 <<< 2
237 iex> 1 <<< -2
[all …]
/dports/lang/elixir/elixir-1.12.3/lib/elixir/lib/
H A Dinteger.ex27 iex> Integer.is_odd(5)
30 iex> Integer.is_odd(6)
33 iex> Integer.is_odd(-5)
36 iex> Integer.is_odd(0)
52 iex> Integer.is_even(10)
55 iex> Integer.is_even(5)
61 iex> Integer.is_even(0)
78 iex> Integer.pow(2, 0)
80 iex> Integer.pow(2, 1)
89 iex> Integer.pow(3, 4)
[all …]
H A Dbitwise.ex11 iex> use Bitwise
26 iex> 1 &&& 1
34 iex> odd? = fn
38 iex> odd?.(1)
70 iex> bnot(2)
92 iex> ~~~2
131 iex> 9 &&& 3
167 iex> 9 ||| 3
234 iex> 1 <<< 2
237 iex> 1 <<< -2
[all …]
/dports/devel/elixir-smppex/smppex-2.2.9/lib/smppex/
H A Dpdu.ex41 iex(1)> SMPPEX.Pdu.new(1)
80 iex(1)> pdu = SMPPEX.Pdu.new(1)
103 iex(1)> pdu = SMPPEX.Pdu.new(1)
252 iex(1)> pdu = SMPPEX.Pdu.new(4)
366 iex(1)> pdu = SMPPEX.Pdu.new(4)
367 iex(2)> SMPPEX.Pdu.resp?(pdu)
370 iex(4)> SMPPEX.Pdu.resp?(pdu)
405 iex(2)> SMPPEX.Pdu.bind?(pdu)
408 iex(4)> SMPPEX.Pdu.bind?(pdu)
466 iex(2)> SMPPEX.Pdu.source(pdu)
[all …]
/dports/shells/fish/fish-3.3.1/share/completions/
H A Diex.fish1 complete -f -c iex -s v -d "Prints version and exit"
2 complete -f -c iex -s e -d "Evaluates the given command"
3 complete -c iex -s r -d "Requires the given files/patterns"
4 complete -c iex -s S -d "Finds and executes the given script"
5 complete -c iex -s pr -d "Requires the given files/patterns in parallel"
6 complete -c iex -s pa -d "Prepends the given path to Erlang code path"
7 complete -c iex -s pz -d "Appends the given path to Erlang code path"
8 complete -c iex -l app -d "Start the given app and its dependencies"
9 complete -f -c iex -l erl -d "Switches to be passed down to erlang"
13 complete -f -c iex -l hidden -d "Makes a hidden node"
[all …]
/dports/lang/elixir/elixir-1.12.3/lib/ex_unit/test/ex_unit/
H A Ddoc_test_test.exs19 iex> one()
21 iex> one() + 1
41 iex> a = 1
44 iex> a + b
88 iex> 1 + ""
90 iex> 2 + ""
99 iex> one()
107 iex> two()
118 iex> 1 + 1
123 iex> one()
[all …]
/dports/devel/elixir-inflex/inflex-1.4.1/
H A DREADME.md44 Here are some basic examples from `iex`:
48 iex(1)> Inflex.singularize("dogs")
51 iex(2)> Inflex.pluralize("dog")
54 iex(3)> Inflex.singularize("people")
57 iex(4)> Inflex.pluralize("person")
67 iex(1)> Inflex.pluralize("piano")
70 iex(2)> Inflex.pluralize("hero")
73 iex(3)> Inflex.pluralize("butterfly")
76 iex(4)> Inflex.pluralize("monkey")
84 iex(1)> Inflex.inflect("child", 1)
[all …]
/dports/lang/elixir-devel/elixir-1.13.1/lib/ex_unit/test/ex_unit/
H A Ddoc_test_test.exs19 iex> one()
21 iex> one() + 1
41 iex> a = 1
44 iex> a + b
96 iex> 1 + ""
98 iex> 2 + ""
107 iex> one()
115 iex> two()
126 iex> 1 + 1
131 iex> one()
[all …]
/dports/devel/elixir-calendar/calendar-0.17.4/lib/calendar/
H A Ddate.ex26 iex> from_erl({2014,12,27})
29 iex> from_erl({2014,99,99})
44 iex> from_erl! {2014,12,27}
478 iex> {2015, 7, 6} |> monday?
480 iex> {2015, 7, 7} |> monday?
528 iex> {2015, 7, 7} |> friday?
552 iex> {2015, 7, 7} |> sunday?
561 iex> from_ordinal(2015, 1)
585 iex> from_ordinal!(2015, 1)
602 iex> {2015, 7, 12} |> to_s
[all …]
/dports/devel/elixir-decimal/decimal-1.4.1/
H A DREADME.md22 iex> alias Decimal, as: D
24 iex> D.add(D.new(6), D.new(7))
26 iex> D.div(D.new(1), D.new(3))
48 iex> D.get_context
58 iex> Decimal.get_context
84 iex> D.div(D.new(31), D.new(2))
100 iex> D.get_context.traps
102 iex> D.get_context.flags
106 iex> D.get_context.flags
126 iex> D.get_context.traps
[all …]
/dports/devel/elixir-csv/csv-2.1.1/lib/
H A Dcsv.ex51 iex> |> File.stream!
52 iex> |> CSV.decode
53 iex> |> Enum.take(2)
60 iex> |> File.stream!
61 iex> |> CSV.decode
62 iex> |> Enum.take(2)
78 iex> |> Enum.take(2)
90 iex> |> Enum.take(2)
140 iex> |> CSV.decode!
149 iex> |> CSV.decode!
[all …]
/dports/science/nwchem/nwchem-7b21660b82ebd85ef659f6fba7e1e73433b0bd0a/src/mcscf/detci_sym/
H A Ddetci_spin.F180 do iex=1,nexa
181 eij(exa(6,iex,istra),exa(5,iex,istra)) = exa(1,iex,istra)
182 pij(exa(6,iex,istra),exa(5,iex,istra)) = exa(4,iex,istra)
188 do iex=1,nexb
285 do iex=1,nexa
286 eij(exa(6,iex,istra),exa(5,iex,istra)) = exa(1,iex,istra)
287 pij(exa(6,iex,istra),exa(5,iex,istra)) = exa(4,iex,istra)
299 do iex=1,nexb
300 iib = exb(5,iex,istrb)
301 jjb = exb(6,iex,istrb)
[all …]
/dports/science/nwchem-data/nwchem-7.0.2-release/src/mcscf/detci_sym/
H A Ddetci_spin.F180 do iex=1,nexa
181 eij(exa(6,iex,istra),exa(5,iex,istra)) = exa(1,iex,istra)
182 pij(exa(6,iex,istra),exa(5,iex,istra)) = exa(4,iex,istra)
188 do iex=1,nexb
285 do iex=1,nexa
286 eij(exa(6,iex,istra),exa(5,iex,istra)) = exa(1,iex,istra)
287 pij(exa(6,iex,istra),exa(5,iex,istra)) = exa(4,iex,istra)
299 do iex=1,nexb
300 iib = exb(5,iex,istrb)
301 jjb = exb(6,iex,istrb)
[all …]
/dports/science/nwchem-data/nwchem-7.0.2-release/src/mcscf/detci/
H A Ddetci_spin.F180 do iex=1,nexa
181 eij(exa(6,iex,istra),exa(5,iex,istra)) = exa(1,iex,istra)
182 pij(exa(6,iex,istra),exa(5,iex,istra)) = exa(4,iex,istra)
188 do iex=1,nexb
287 do iex=1,nexa
288 eij(exa(6,iex,istra),exa(5,iex,istra)) = exa(1,iex,istra)
289 pij(exa(6,iex,istra),exa(5,iex,istra)) = exa(4,iex,istra)
301 do iex=1,nexb
302 iib = exb(5,iex,istrb)
303 jjb = exb(6,iex,istrb)
[all …]
/dports/science/nwchem/nwchem-7b21660b82ebd85ef659f6fba7e1e73433b0bd0a/src/mcscf/detci/
H A Ddetci_spin.F180 do iex=1,nexa
181 eij(exa(6,iex,istra),exa(5,iex,istra)) = exa(1,iex,istra)
182 pij(exa(6,iex,istra),exa(5,iex,istra)) = exa(4,iex,istra)
188 do iex=1,nexb
287 do iex=1,nexa
288 eij(exa(6,iex,istra),exa(5,iex,istra)) = exa(1,iex,istra)
289 pij(exa(6,iex,istra),exa(5,iex,istra)) = exa(4,iex,istra)
301 do iex=1,nexb
302 iib = exb(5,iex,istrb)
303 jjb = exb(6,iex,istrb)
[all …]
/dports/lang/elixir/elixir-1.12.3/lib/elixir/lib/calendar/
H A Dtime.ex9 iex> ~T[23:00:07.001]
15 iex> time = ~T[23:00:07.001]
16 iex> time.hour
18 iex> time.microsecond
56 iex> time = Time.utc_now()
57 iex> time.hour >= 0
91 iex> Time.new(0, 0, 0, 0)
93 iex> Time.new(23, 59, 59, 999_999)
96 iex> Time.new(24, 59, 59, 999_999)
98 iex> Time.new(23, 60, 59, 999_999)
[all …]
/dports/lang/elixir-devel/elixir-1.13.1/lib/elixir/lib/calendar/
H A Dtime.ex9 iex> ~T[23:00:07.001]
15 iex> time = ~T[23:00:07.001]
16 iex> time.hour
18 iex> time.microsecond
56 iex> time = Time.utc_now()
57 iex> time.hour >= 0
91 iex> Time.new(0, 0, 0, 0)
93 iex> Time.new(23, 59, 59, 999_999)
96 iex> Time.new(24, 59, 59, 999_999)
98 iex> Time.new(23, 60, 59, 999_999)
[all …]
/dports/astro/gpsman/gpsman-6.4.4.2/manual/html/info/
H A Dinstupdate.tcl159 set iex ""
161 if { [catch {set iex [exec which gpsman]}] && \
165 set iex $f
172 if { $iex == "" || [catch {set v [exec $iex show version]}] || \
176 gets stdin iex
177 if { [file pathtype $iex] != "absolute" || \
183 } elseif { $iex == "" } {
186 gets stdin iex
193 set isd [FindValues SRCDIR $iex]
218 set fiex $iex
[all …]

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