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Searched refs:allowSubprocess (Results 1 – 25 of 27) sorted by relevance

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/dports/biology/bbmap/bbmap/current/fileIO/
H A DReadWrite.java90 private final boolean allowSubprocess; field in ReadWrite.WriteObjectThread
94 allowSubprocess=allowSubprocess_; in WriteObjectThread()
102 writeAsync(x, fname, allowSubprocess); in run()
378 allowSubprocess=(allowSubprocess && Shared.threads()>1); in getOutputStream() field in ReadWrite
844 allowSubprocess=(allowSubprocess && Shared.threads()>1); in getInputStream()
1019 if(allowSubprocess && Shared.threads()>2){
1195 try {in=getBZipInputStream2(fname, allowSubprocess);}
1282 X x=(X)readObject(fname, allowSubprocess); in read()
1287 X[] x=(X[])readObject(fname, allowSubprocess); in readArray()
1292 X[][] x=(X[][])readObject(fname, allowSubprocess); in readArray2()
[all …]
H A DByteFile.java16 public static final ByteFile makeByteFile1(String fname, boolean allowSubprocess){ in makeByteFile1() argument
17 FileFormat ff=FileFormat.testInput(fname, FileFormat.TEXT, null, allowSubprocess, false); in makeByteFile1()
21 public static final ByteFile makeByteFile(String fname, boolean allowSubprocess){ in makeByteFile() argument
22 FileFormat ff=FileFormat.testInput(fname, FileFormat.TEXT, null, allowSubprocess, false); in makeByteFile()
121 public final boolean allowSubprocess(){return ff.allowSubprocess();} in allowSubprocess() method in ByteFile
H A DFileFormat.java105 …public static FileFormat testInput(String fname, String overrideExtension, boolean allowSubprocess… in testInput() argument
106 …if(verbose){System.err.println("testInputA("+fname+", "+overrideExtension+", "+allowSubprocess+")"… in testInput()
107 return testInput(fname, FASTQ, overrideExtension, allowSubprocess, true); in testInput()
114 …ffa[i]=testInput(fname.get(i), defaultFormat, overrideExtension, allowSubprocess, allowFileRead, f… in testInputList()
122 array[i]=testInput(fnames[i], defaultFormat, overrideExtension, allowSubprocess, allowFileRead); in testInput()
129 return testInput(fname, defaultFormat, overrideExtension, allowSubprocess, allowFileRead, false); in testInput()
159 int overrideCompression, boolean allowSubprocess, boolean allowFileRead, boolean forceFileRead){ in testInput() argument
252 allowSubprocess=allowSubprocess_; in FileFormat()
285 sb.append("sub="+(allowSubprocess ? "t" : "f")).append(','); in toString()
752 public final boolean allowSubprocess(){return allowSubprocess;} in allowSubprocess() method in FileFormat
[all …]
H A DTextFile.java111 allowSubprocess=ff.allowSubprocess(); in TextFile()
120 allowSubprocess=allowSubprocess_; in TextFile()
206 errorState|=ReadWrite.finishReading(is, name, allowSubprocess, br, isr); in close()
280 is=ReadWrite.getInputStream(name, true, allowSubprocess); in open()
295 private final boolean allowSubprocess; field in TextFile
H A DTextStreamWriter.java49 allowSubprocess=ff.allowSubprocess(); in TextStreamWriter()
55 myOutstream=ReadWrite.getOutputStream(fname, append, true, allowSubprocess); in TextStreamWriter()
56 …System.err.println("Created output stream for "+fname+", "+append+", "+true+", "+allowSubprocess);} in TextStreamWriter()
122 ReadWrite.finishWriting(myWriter, myOutstream, fname, allowSubprocess); in run()
303 public final boolean allowSubprocess; field in TextStreamWriter
H A DQuickFile.java108 …errorState|=ReadWrite.finishReading(is, name(), (allowSubprocess() || FileFormat.isBamFile(name())… in close()
247 is=ReadWrite.getInputStream(name(), BUFFERED, allowSubprocess()); in open()
299 public final boolean allowSubprocess(){return ff.allowSubprocess();} in allowSubprocess() method in QuickFile
H A DByteStreamWriter.java83 allowSubprocess=ff.allowSubprocess(); in ByteStreamWriter()
92 outstream=ReadWrite.getOutputStream(fname, append, true, allowSubprocess); in ByteStreamWriter()
140 ReadWrite.finishWriting(null, outstream, fname, allowSubprocess); in run()
662 public final boolean allowSubprocess; field in ByteStreamWriter
H A DByteFile1.java117 …errorState|=ReadWrite.finishReading(is, name(), (allowSubprocess() || FileFormat.isBamFile(name())… in close()
330 is=ReadWrite.getInputStream(name(), BUFFERED, allowSubprocess()); in open()
/dports/biology/bbmap/bbmap/current/align2/
H A DBlock.java92 ReadWrite.writeObjectInThread(sites, fname, allowSubprocess); in write()
94 ReadWrite.writeObjectInThread(starts, fname+"2.gz", allowSubprocess); in write()
102 ReadWrite.writeObjectInThread(starts, fname+"2.gz", allowSubprocess); in write()
105 ReadWrite.writeAsync(starts, fname+"2.gz", allowSubprocess); in write()
167 private static boolean allowSubprocess=false; field in Block
/dports/biology/bbmap/bbmap/current/stream/
H A DReadStreamWriter.java50 allowSubprocess=ff.allowSubprocess(); in ReadStreamWriter()
58 …eam=ReadWrite.getOutputStream(qfname, (ff==null ? false : ff.append()), buffered, allowSubprocess); in ReadStreamWriter()
73 …if(!allowSubprocess){System.err.println("Warning! Spawning a samtools process when allowSubprocess… in ReadStreamWriter()
319 protected final boolean allowSubprocess; field in ReadStreamWriter
H A DMultiCros.java72 allowSubprocess=allowSubprocess_; in MultiCros()
139 …final FileFormat ff1=FileFormat.testOutput(s1, defaultFormat, null, allowSubprocess, overwrite, ap… in makeStream()
140 …final FileFormat ff2=FileFormat.testOutput(s2, defaultFormat, null, allowSubprocess, overwrite, ap… in makeStream()
178 final boolean allowSubprocess; field in MultiCros
H A DFastaShredInputStream.java56 allowSubprocess=ff.allowSubprocess(); in FastaShredInputStream()
189 ByteFile bf=ByteFile.makeByteFile(name, allowSubprocess); in open()
224 public final boolean allowSubprocess; field in FastaShredInputStream
H A DCrisContainer.java12 public CrisContainer(String fname, Comparator<Read> comparator_, boolean allowSubprocess){ in CrisContainer() argument
14 FileFormat ff=FileFormat.testInput(fname, FileFormat.FASTQ, null, allowSubprocess, true); in CrisContainer()
H A DBufferedMultiCros.java60 allowSubprocess=allowSubprocess_; in BufferedMultiCros()
217 final boolean allowSubprocess; field in BufferedMultiCros
H A DFastaReadInputStream.java66 allowSubprocess=ff.allowSubprocess(); in FastaReadInputStream()
147 errorState|=ReadWrite.finishReading(ins, name, allowSubprocess); in close()
507 ins=ReadWrite.getInputStream(name, true, allowSubprocess); in open()
555 public final boolean allowSubprocess; field in FastaReadInputStream
H A DConcurrentReadInputStream.java31 …eam getReadInputStream(long maxReads, boolean keepSamHeader, boolean allowSubprocess, String...arg… in getReadInputStream() argument
44 final FileFormat ff1=FileFormat.testInput(in1, null, allowSubprocess); in getReadInputStream()
45 final FileFormat ff2=FileFormat.testInput(in2, null, allowSubprocess); in getReadInputStream()
H A DMultiCros2.java166 ff1=FileFormat.testOutput(s1, defaultFormat, null, allowSubprocess, false, true, false); in Buffer()
167 ff2=FileFormat.testOutput(s2, defaultFormat, null, allowSubprocess, false, true, false); in Buffer()
H A DMultiCros3.java210 ff1=FileFormat.testOutput(s1, defaultFormat, null, allowSubprocess, false, true, false); in Buffer()
211 ff2=FileFormat.testOutput(s2, defaultFormat, null, allowSubprocess, false, true, false); in Buffer()
H A DReadStreamByteWriter.java118 …ReadWrite.finishWriting(null, job.outstream, fname, allowSubprocess); //TODO: This should be job.… in processJobs()
143 ReadWrite.finishWriting(null, myOutstream, fname, allowSubprocess); in finishWriting()
150 ReadWrite.finishWriting(null, myQOutstream, qfname, allowSubprocess); in finishWriting()
/dports/biology/bbmap/bbmap/current/sort/
H A DSortByName.java522 private ArrayList<String> mergeRecursive(final ArrayList<String> inList, boolean allowSubprocess){ in mergeRecursive() argument
545 mergeRecursiveInner(subList, ffoutTemp, null, deleteAfterMerge, allowSubprocess); in mergeRecursive()
561 …, FileFormat ffoutTemp1, FileFormat ffoutTemp2, boolean deleteAfterMerge, boolean allowSubprocess){ in mergeRecursiveInner() argument
562 …/*null, */ffoutTemp1, ffoutTemp2, deleteAfterMerge, useSharedHeader, allowSubprocess, outstream, m… in mergeRecursiveInner()
580 …Dump(ArrayList<String> fnames, /*IntList dumpCount, */boolean useHeader, boolean allowSubprocess) { in mergeAndDump() argument
585 fnames=mergeRecursive(fnames, allowSubprocess); in mergeAndDump()
587 …return mergeAndDump(fnames, /*dumpCount,*/ ffout1, ffout2, delete, useHeader, allowSubprocess, out… in mergeAndDump()
591 …boolean deleteAfterMerge, boolean useHeader, boolean allowSubprocess, PrintStream outstream, final… in mergeAndDump() argument
623 CrisContainer cc=new CrisContainer(fname, /*size, */comparator, allowSubprocess); in mergeAndDump()
/dports/biology/bbmap/bbmap/current/driver/
H A DConcatenateTextFiles.java167 ReadWrite.finishWriting(writer, os, fname, allowSubprocess); in run()
189 public static boolean allowSubprocess=true; field in ConcatenateTextFiles
/dports/biology/bbmap/bbmap/current/var/
H A DGenerateVarlets2.java233 boolean allowSubprocess=false; in writeList()
234 OutputStream os=ReadWrite.getOutputStream(fname, true, true, allowSubprocess); in writeList()
241 ReadWrite.finishWriting(pw, os, fname, allowSubprocess); in writeList()
H A DGenerateVarlets3.java378 boolean allowSubprocess=false;
379 OutputStream os=ReadWrite.getOutputStream(fname, true, true, allowSubprocess);
386 ReadWrite.finishWriting(pw, os, fname, allowSubprocess);
/dports/biology/bbmap/bbmap/current/jgi/
H A DCrossContaminate.java404 public Vessel(String fname_, boolean allowSubprocess){ in Vessel() argument
406 …ff=FileFormat.testOutput(fname, FileFormat.FASTQ, null, allowSubprocess, overwrite, append, false); in Vessel()
/dports/biology/bbmap/bbmap/current/var2/
H A DMergeSamples.java129 final boolean allowSubprocess=(ways<=4); in mergeFiles()
132 FileFormat ff=FileFormat.testInput(pair.b, FileFormat.VCF, null, allowSubprocess, false); in mergeFiles()

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