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Searched refs:ffin1 (Results 1 – 25 of 111) sorted by relevance

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/dports/biology/bbmap/bbmap/current/template/
H A DA_Sample2.java74 ffin1=FileFormat.testInput(in1, FileFormat.FASTQ, null, true, true); in A_Sample2()
81 cris=ConcurrentReadInputStream.getReadInputStream(maxReads, true, ffin1, null); in process()
108 assert((ffin1==null || ffin1.samOrBam()) || (r.mate!=null)==cris.paired()); in process()
148 private final FileFormat ffin1; field in A_Sample2
H A DA_SampleSummary.java74 ffin1=FileFormat.testInput(in1, FileFormat.FASTQ, null, true, true); in A_SampleSummary()
81 cris=ConcurrentReadInputStream.getReadInputStream(maxReads, true, ffin1, null); in process()
94 assert((ffin1==null || ffin1.samOrBam()) || (r.mate!=null)==cris.paired()); in process()
145 private final FileFormat ffin1; field in A_SampleSummary
H A DA_SampleD.java83 ffin1=FileFormat.testInput(in1, FileFormat.FASTQ, null, true, true); in A_SampleD()
89 maxReads, false, ffin1, null, Shared.USE_MPI, Shared.MPI_KEEP_ALL); in process()
116 assert((ffin1==null || ffin1.samOrBam()) || (r.mate!=null)==crisD.paired()); in process()
157 private final FileFormat ffin1; field in A_SampleD
H A DA_Sample_Unpaired.java128 ffin1=FileFormat.testInput(in1, FileFormat.FASTQ, extin, true, true); in A_Sample_Unpaired()
135 cris=ConcurrentReadInputStream.getReadInputStream(maxReads, true, ffin1, null, qfin1, null); in process()
141 …if(!ffin1.samOrBam()){outstream.println("Input is being processed as "+(paired ? "paired" : "unpai… in process()
166 assert((ffin1==null || ffin1.samOrBam()) || (r.mate!=null)==cris.paired()); in process()
237 private final FileFormat ffin1; field in A_Sample_Unpaired
H A DA_Sample.java107 ffin1=FileFormat.testInput(in1, FileFormat.FASTQ, extin, true, true); in A_Sample()
275 …ConcurrentReadInputStream cris=ConcurrentReadInputStream.getReadInputStream(maxReads, true, ffin1,… in makeCris()
279 …if(!ffin1.samOrBam()){outstream.println("Input is being processed as "+(paired ? "paired" : "unpai… in makeCris()
290 if(pairedInput && out2==null && (in1!=null && !ffin1.samOrBam() && !ffout1.samOrBam())){ in makeCros()
311 assert(ffin1.samOrBam() || (r.mate!=null)==cris.paired()); in processInner()
441 private final FileFormat ffin1; field in A_Sample
H A DBBTool_ST.java162 ffin1=FileFormat.testInput(in1, FileFormat.FASTQ, extin, true, true); in BBTool_ST()
276 cris=ConcurrentReadInputStream.getReadInputStream(maxReads, true, ffin1, ffin2, qfin1, qfin2); in startup()
281 …if(!ffin1.samOrBam()){outstream.println("Input is being processed as "+(paired ? "paired" : "unpai… in startup()
347 assert((ffin1==null || ffin1.samOrBam()) || (r.mate!=null)==cris.paired()); in processInner()
435 protected final FileFormat ffin1; field in BBTool_ST
/dports/biology/bbmap/bbmap/current/prok/
H A DFilterSilva.java133 ffin1=FileFormat.testInput(in1, FileFormat.FASTQ, extin, true, true); in FilterSilva()
142 cris=ConcurrentReadInputStream.getReadInputStream(maxReads, true, ffin1, null); in process()
148 …if(!ffin1.samOrBam()){outstream.println("Input is being processed as "+(paired ? "paired" : "unpai… in process()
173 assert((ffin1==null || ffin1.samOrBam()) || (r.mate!=null)==cris.paired()); in process()
249 private final FileFormat ffin1; field in FilterSilva
/dports/biology/bbmap/bbmap/current/tax/
H A DFilterByTaxa.java194 ffin1=FileFormat.testInput(in1, FileFormat.FASTA, extin, true, true); in FilterByTaxa()
214 cris=ConcurrentReadInputStream.getReadInputStream(maxReads, true, ffin1, ffin2, qfin1, qfin2); in process()
219 …if(!ffin1.samOrBam()){outstream.println("Input is being processed as "+(paired ? "paired" : "unpai… in process()
226 if(cris.paired() && out2==null && (in1!=null && !ffin1.samOrBam() && !ffout1.samOrBam())){ in process()
282 assert((ffin1==null || ffin1.samOrBam()) || (r.mate!=null)==cris.paired()); in processInner()
415 private final FileFormat ffin1; field in FilterByTaxa
H A DPrintTaxonomy.java152 ffin1=FileFormat.testInput(in1, FileFormat.TEXT, null, true, false); in PrintTaxonomy()
184 if(ffin1!=null){ in process()
185 if(ffin1.fasta() || ffin1.fastq() || ffin1.samOrBam() || ffin1.scarf()){ in process()
188 processFile(new TextFile(ffin1), tsw); in process()
245 cris=ConcurrentReadInputStream.getReadInputStream(maxReads, true, ffin1, null); in processReads()
535 private final FileFormat ffin1;
H A DSplitByTaxa.java194 ffin1=FileFormat.testInput(in1, FileFormat.FASTQ, extin, true, true); in SplitByTaxa()
211 cris=ConcurrentReadInputStream.getReadInputStream(maxReads, true, ffin1, ffin2, null, null); in process()
216 …if(!ffin1.samOrBam()){outstream.println("Input is being processed as "+(paired ? "paired" : "unpai… in process()
262 assert((ffin1==null || ffin1.samOrBam()) || (r.mate!=null)==cris.paired()); in processInner()
363 private final FileFormat ffin1; field in SplitByTaxa
/dports/biology/bbmap/bbmap/current/jgi/
H A DIdentityMatrix.java89 ffin1=FileFormat.testInput(in1, FileFormat.FASTQ, null, true, true); in IdentityMatrix()
162 cris=ConcurrentReadInputStream.getReadInputStream(maxReads, true, ffin1, null); in load()
179 assert((ffin1==null || ffin1.samOrBam()) || (r.mate!=null)==cris.paired()); in load()
233 assert((ffin1==null || ffin1.samOrBam()) || (r.mate!=null)==cris.paired()); in run()
292 private final FileFormat ffin1; field in IdentityMatrix
H A DTetramerFrequencies.java101 ffin1=FileFormat.testInput(in1, FileFormat.FASTQ, null, true, true); in TetramerFrequencies()
102 assert(ffin1!=null) : "No input file."; in TetramerFrequencies()
103 assert(ffin1.exists() && ffin1.canRead()) : "Cannot read input file "+in1+"."; in TetramerFrequencies()
135 cris=ConcurrentReadInputStream.getReadInputStream(maxReads, true, ffin1, null); in process()
146 assert((ffin1==null || ffin1.samOrBam()) || (r.mate!=null)==cris.paired()); in process()
522 private final FileFormat ffin1;
H A DPartitionReads.java226 ffin1=FileFormat.testInput(in1, FileFormat.FASTQ, extin, true, true); in PartitionReads()
229 …useSharedHeader=(ffin1.samOrBam() && ffout1!=null && ffout1.length>0 && ffout1[0]!=null && ffout1[… in PartitionReads()
242 cris=ConcurrentReadInputStream.getReadInputStream(maxReads, true, ffin1, ffin2, qfin1, qfin2); in process()
247 …if(!ffin1.samOrBam()){outstream.println("Input is being processed as "+(paired ? "paired" : "unpai… in process()
299 assert((ffin1==null || ffin1.samOrBam()) || (r.mate!=null)==cris.paired()); in processInner()
410 private final FileFormat ffin1; field in PartitionReads
H A DKeepBestCopy.java134 ffin1=FileFormat.testInput(in1, FileFormat.FASTA, extin, true, true); in KeepBestCopy()
139 cris=ConcurrentReadInputStream.getReadInputStream(maxReads, true, ffin1, null, qfin1, null); in makeCris()
149 …if(!ffin1.samOrBam()){outstream.println("Input is being processed as "+(paired ? "paired" : "unpai… in process()
163 assert((ffin1==null || ffin1.samOrBam()) || (r.mate!=null)==cris.paired()); in process()
277 private final FileFormat ffin1; field in KeepBestCopy
H A DReplaceHeaders.java201 ffin1=FileFormat.testInput(in1, FileFormat.FASTQ, extin, true, true); in ReplaceHeaders()
219 cris=ConcurrentReadInputStream.getReadInputStream(maxReads, true, ffin1, ffin2, qfin1, qfin2); in process()
224 …if(!ffin1.samOrBam()){outstream.println("Input is being processed as "+(paired ? "paired" : "unpai… in process()
243 if(cris.paired() && out2==null && (in1!=null && !ffin1.samOrBam() && !ffout1.samOrBam())){ in process()
300 assert((ffin1==null || ffin1.samOrBam()) || (r.mate!=null)==cris.paired()); in processInner()
435 private final FileFormat ffin1; field in ReplaceHeaders
H A DCutPrimers.java83 ffin1=FileFormat.testInput(in1, FileFormat.FASTQ, null, true, true); in CutPrimers()
90 cris=ConcurrentReadInputStream.getReadInputStream(maxReads, true, ffin1, null); in process()
120 assert((ffin1==null || ffin1.samOrBam()) || (r.mate!=null)==cris.paired()); in process()
224 private final FileFormat ffin1; field in CutPrimers
/dports/biology/bbmap/bbmap/current/driver/
H A DReduceSilva.java120 ffin1=FileFormat.testInput(in1, FileFormat.FASTQ, extin, true, true); in ReduceSilva()
144 cris=ConcurrentReadInputStream.getReadInputStream(maxReads, true, ffin1, null); in process()
149 …if(!ffin1.samOrBam()){outstream.println("Input is being processed as "+(paired ? "paired" : "unpai… in process()
217 assert((ffin1==null || ffin1.samOrBam()) || (r.mate!=null)==cris.paired()); in processInner()
304 private final FileFormat ffin1; field in ReduceSilva
H A DFilterReadsByName.java233 ffin1=FileFormat.testInput(in1, FileFormat.FASTQ, extin, true, true); in FilterReadsByName()
236 if(ffin1!=null && ffout1!=null && ffin1.samOrBam() && ffout1.samOrBam()){ in FilterReadsByName()
254 …cris=ConcurrentReadInputStream.getReadInputStream(maxReads, useSharedHeader, ffin1, ffin2, qfin1, … in process()
260 …if(!ffin1.samOrBam()){outstream.println("Input is being processed as "+(paired ? "paired" : "unpai… in process()
293 assert((ffin1==null || ffin1.samOrBam()) || (r.mate!=null)==cris.paired()); in process()
425 private final FileFormat ffin1; field in FilterReadsByName
H A DPlotGC.java125 ffin1=FileFormat.testInput(in1, FileFormat.FASTA, extin, true, true); in PlotGC()
132 cris=ConcurrentReadInputStream.getReadInputStream(maxReads, true, ffin1, null, null, null); in process()
156 assert((ffin1==null || ffin1.samOrBam()) || (r.mate!=null)==cris.paired()); in process()
266 private final FileFormat ffin1; field in PlotGC
/dports/biology/bbmap/bbmap/current/icecream/
H A DIceCreamGrader.java115 ffin1=FileFormat.testInput(in1, FileFormat.FASTQ, extin, true, true); in IceCreamGrader()
122 cris=ConcurrentReadInputStream.getReadInputStream(maxReads, true, ffin1, null); in process()
139 assert((ffin1==null || ffin1.samOrBam()) || (r.mate!=null)==cris.paired()); in process()
218 private final FileFormat ffin1; field in IceCreamGrader
/dports/biology/bbmap/bbmap/current/sketch/
H A DInvertKey.java142 ffin1=FileFormat.testInput(in1, FileFormat.FASTA, null, true, true); in InvertKey()
176 cris=ConcurrentReadInputStream.getReadInputStream(maxReads, true, ffin1, null, null, null); in process()
182 …if(!ffin1.samOrBam()){outstream.println("Input is being processed as "+(paired ? "paired" : "unpai… in process()
205 assert((ffin1==null || ffin1.samOrBam()) || (r.mate!=null)==cris.paired()); in process()
303 private final FileFormat ffin1; field in InvertKey
/dports/biology/bbmap/bbmap/current/ml/
H A DProcessBBMergeHeaders.java72 ffin1=FileFormat.testInput(in1, FileFormat.FASTQ, null, true, true); in ProcessBBMergeHeaders()
79 cris=ConcurrentReadInputStream.getReadInputStream(maxReads, false, ffin1, null); in process()
101 assert((ffin1==null || ffin1.samOrBam()) || (r.mate!=null)==cris.paired()); in process()
251 private final FileFormat ffin1; field in ProcessBBMergeHeaders
/dports/biology/bbmap/bbmap/current/var2/
H A DCompareVCF.java120 ffin1=new FileFormat[in1.length]; in CompareVCF()
122 ffin1[i]=FileFormat.testInput(in1[i], FileFormat.VCF, null, true, true); in CompareVCF()
164 for(FileFormat ff : ffin1){ in union()
172 for(FileFormat ff : ffin1){ in intersection()
182 for(FileFormat ff : ffin1){ in difference()
282 private final FileFormat ffin1[]; field in CompareVCF
/dports/biology/bbmap/bbmap/current/hiseq/
H A DPlotFlowCell.java188 ffin1=FileFormat.testInput(in1, FileFormat.FASTQ, extin, true, true); in PlotFlowCell()
234 cris=ConcurrentReadInputStream.getReadInputStream(maxReads, true, ffin1, ffin2, qfin1, qfin2); in loadKmers()
259 cris=ConcurrentReadInputStream.getReadInputStream(maxReads, true, ffin1, ffin2, qfin1, qfin2); in fillTiles()
300 assert((ffin1==null || ffin1.samOrBam()) || (r.mate!=null)==cris.paired()); in loadKmersInner()
368 assert((ffin1==null || ffin1.samOrBam()) || (r.mate!=null)==cris.paired()); in fillTilesInner()
568 private final FileFormat ffin1; field in PlotFlowCell
/dports/biology/bbmap/bbmap/current/jasper/
H A DKmerPosition.java85 ffin1=FileFormat.testInput(in1, FileFormat.FASTQ, null, true, true); in KmerPosition()
95 cris=ConcurrentReadInputStream.getReadInputStream(maxReads, true, ffin1, ffin2); in process()
110 assert((ffin1==null || ffin1.samOrBam()) || (r.mate!=null)==cris.paired()); in process()
234 private final FileFormat ffin1; field in KmerPosition

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