| /dports/biology/bbmap/bbmap/current/stream/ |
| H A D | BufferedMultiCros.java | 28 …boolean overwrite_, boolean append_, boolean allowSubprocess_, boolean useSharedHeader_, int defau… in BufferedMultiCros() argument
29 …this(pattern1_, pattern2_, overwrite_, append_, allowSubprocess_, useSharedHeader_, defaultFormat_… in BufferedMultiCros()
45 …boolean overwrite_, boolean append_, boolean allowSubprocess_, boolean useSharedHeader_, int defau… in BufferedMultiCros() argument
60 allowSubprocess=allowSubprocess_; in BufferedMultiCros()
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| H A D | ScarfReadInputStream.java | 20 public ScarfReadInputStream(String fname, boolean allowSubprocess_){ in ScarfReadInputStream() argument
21 this(FileFormat.testInput(fname, FileFormat.SCARF, null, allowSubprocess_, false)); in ScarfReadInputStream()
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| H A D | FastqReadInputStream.java | 20 public FastqReadInputStream(String fname, boolean allowSubprocess_){ in FastqReadInputStream() argument
21 this(FileFormat.testInput(fname, FileFormat.FASTQ, null, allowSubprocess_, false)); in FastqReadInputStream()
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| H A D | HeaderInputStream.java | 28 public HeaderInputStream(String fname, boolean allowSubprocess_){ in HeaderInputStream() argument
29 this(FileFormat.testInput(fname, FileFormat.FASTQ, null, allowSubprocess_, false)); in HeaderInputStream()
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| H A D | OnelineReadInputStream.java | 22 public OnelineReadInputStream(String fname, boolean allowSubprocess_){ in OnelineReadInputStream() argument
23 this(FileFormat.testInput(fname, FileFormat.ONELINE, null, allowSubprocess_, false)); in OnelineReadInputStream()
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| H A D | EmblReadInputStream.java | 23 public EmblReadInputStream(String fname, boolean allowSubprocess_){ in EmblReadInputStream() argument
24 this(FileFormat.testInput(fname, FileFormat.EMBL, null, allowSubprocess_, false)); in EmblReadInputStream()
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| H A D | GbkReadInputStream.java | 23 public GbkReadInputStream(String fname, boolean allowSubprocess_){ in GbkReadInputStream() argument
24 this(FileFormat.testInput(fname, FileFormat.GBK, null, allowSubprocess_, false)); in GbkReadInputStream()
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| H A D | MultiCros.java | 58 …boolean ordered_, boolean overwrite_, boolean append_, boolean allowSubprocess_, boolean useShared… in MultiCros() argument
72 allowSubprocess=allowSubprocess_; in MultiCros()
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| H A D | FastaShredInputStream.java | 43 public FastaShredInputStream(String fname, boolean amino_, boolean allowSubprocess_, long maxdata){ in FastaShredInputStream() argument
44 …this(FileFormat.testInput(fname, FileFormat.FASTA, FileFormat.FASTA, 0, allowSubprocess_, false, f… in FastaShredInputStream()
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| H A D | SamReadInputStream.java | 24 …ReadInputStream(String fname, boolean loadHeader_, boolean interleaved_, boolean allowSubprocess_){ in SamReadInputStream() argument
25 …this(FileFormat.testInput(fname, FileFormat.SAM, null, allowSubprocess_, false), loadHeader_, inte… in SamReadInputStream()
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| H A D | MultiCros2.java | 61 …boolean overwrite_, boolean append_, boolean allowSubprocess_, boolean useSharedHeader_, int defau… in MultiCros2() argument
62 …super(pattern1_, pattern2_, overwrite_, append_, allowSubprocess_, useSharedHeader_, defaultFormat… in MultiCros2()
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| H A D | FastaQualReadInputStream.java | 28 public FastaQualReadInputStream(String fname, String qfname, boolean allowSubprocess_){ in FastaQualReadInputStream() argument
29 this(FileFormat.testInput(fname, FileFormat.FASTA, null, allowSubprocess_, false), qfname); in FastaQualReadInputStream()
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| H A D | MultiCros3.java | 75 …boolean overwrite_, boolean append_, boolean allowSubprocess_, boolean useSharedHeader_, int defau… in MultiCros3() argument
76 …super(pattern1_, pattern2_, overwrite_, append_, allowSubprocess_, useSharedHeader_, defaultFormat… in MultiCros3()
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| H A D | FastaReadInputStream.java | 52 …tStream(String fname, boolean interleaved_, boolean amino_, boolean allowSubprocess_, long maxdata… in FastaReadInputStream() argument
53 …this(FileFormat.testInput(fname, FileFormat.FASTA, FileFormat.FASTA, 0, allowSubprocess_, false, f… in FastaReadInputStream()
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| /dports/biology/bbmap/bbmap/current/fileIO/ |
| H A D | TextStreamWriter.java | 27 …lic TextStreamWriter(String fname_, boolean overwrite_, boolean append_, boolean allowSubprocess_){ in TextStreamWriter() argument
28 this(fname_, overwrite_, append_, allowSubprocess_, 0); in TextStreamWriter()
31 …amWriter(String fname_, boolean overwrite_, boolean append_, boolean allowSubprocess_, int format){ in TextStreamWriter() argument
32 …this(FileFormat.testOutput(fname_, FileFormat.TEXT, format, 0, allowSubprocess_, overwrite_, appen… in TextStreamWriter()
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| H A D | FileFormat.java | 199 …nt mode_, int defaultFormat, int overrideFormat, int overrideCompression, boolean allowSubprocess_, in FileFormat() argument
206 ", allowSub="+allowSubprocess_+", allowRead="+allowFileRead+", forceFileRead="+forceFileRead+ in FileFormat()
252 allowSubprocess=allowSubprocess_; in FileFormat()
260 …mode_+", "+defaultFormat+", "+overrideFormat+", "+overrideCompression+", "+allowSubprocess_+", "+a… in FileFormat()
262 …mode_+", "+defaultFormat+", "+overrideFormat+", "+overrideCompression+", "+allowSubprocess_+", "+a… in FileFormat()
264 …mode_+", "+defaultFormat+", "+overrideFormat+", "+overrideCompression+", "+allowSubprocess_+", "+a… in FileFormat()
266 …mode_+", "+defaultFormat+", "+overrideFormat+", "+overrideCompression+", "+allowSubprocess_+", "+a… in FileFormat()
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| H A D | ByteStreamWriter.java | 56 …lic ByteStreamWriter(String fname_, boolean overwrite_, boolean append_, boolean allowSubprocess_){ in ByteStreamWriter() argument
57 this(fname_, overwrite_, append_, allowSubprocess_, 0); in ByteStreamWriter()
61 …amWriter(String fname_, boolean overwrite_, boolean append_, boolean allowSubprocess_, int format){ in ByteStreamWriter() argument
62 …this(FileFormat.testOutput(fname_, FileFormat.TEXT, format, 0, allowSubprocess_, overwrite_, appen… in ByteStreamWriter()
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| H A D | TextFile.java | 117 public TextFile(String fname, boolean allowSubprocess_){ in TextFile() argument
120 allowSubprocess=allowSubprocess_; in TextFile()
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| H A D | QuickFile.java | 83 public QuickFile(String fname, boolean allowSubprocess_){ in QuickFile() argument
84 this(FileFormat.testInput(fname, FileFormat.TEXT, null, allowSubprocess_, false)); in QuickFile()
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| H A D | ByteFile1.java | 93 public ByteFile1(String fname, boolean allowSubprocess_){ in ByteFile1() argument
94 this(FileFormat.testInput(fname, FileFormat.TEXT, null, allowSubprocess_, false)); in ByteFile1()
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| H A D | ByteFile2.java | 79 public ByteFile2(String fname, boolean allowSubprocess_){ in ByteFile2() argument
80 this(FileFormat.testInput(fname, FileFormat.TEXT, null, allowSubprocess_, false)); in ByteFile2()
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| H A D | ReadWrite.java | 91 WriteObjectThread(Object x_, String fname_, boolean allowSubprocess_){ in WriteObjectThread() argument
94 allowSubprocess=allowSubprocess_; in WriteObjectThread()
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