add thirdparty binary

binary/centos6/thirdparty/DAZZ_DB/Makefile

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+CFLAGS = -O3 -Wall -Wextra -Wno-unused-result -fno-strict-aliasing
+
+ALL = fasta2DB DB2fasta quiva2DB DB2quiva DBsplit DBdust Catrack DBshow DBstats DBrm simulator \
+      fasta2DAM DAM2fasta DBdump
+
+all: $(ALL)
+
+fasta2DB: fasta2DB.c DB.c DB.h QV.c QV.h
+	gcc $(CFLAGS) -o fasta2DB fasta2DB.c DB.c QV.c -lm
+
+DB2fasta: DB2fasta.c DB.c DB.h QV.c QV.h
+	gcc $(CFLAGS) -o DB2fasta DB2fasta.c DB.c QV.c -lm
+
+quiva2DB: quiva2DB.c DB.c DB.h QV.c QV.h
+	gcc $(CFLAGS) -o quiva2DB quiva2DB.c DB.c QV.c -lm
+
+DB2quiva: DB2quiva.c DB.c DB.h QV.c QV.h
+	gcc $(CFLAGS) -o DB2quiva DB2quiva.c DB.c QV.c -lm
+
+DBsplit: DBsplit.c DB.c DB.h QV.c QV.h
+	gcc $(CFLAGS) -o DBsplit DBsplit.c DB.c QV.c -lm
+
+DBdust: DBdust.c DB.c DB.h QV.c QV.h
+	gcc $(CFLAGS) -o DBdust DBdust.c DB.c QV.c -lm
+
+Catrack: Catrack.c DB.c DB.h QV.c QV.h
+	gcc $(CFLAGS) -o Catrack Catrack.c DB.c QV.c -lm
+
+DBshow: DBshow.c DB.c DB.h QV.c QV.h
+	gcc $(CFLAGS) -o DBshow DBshow.c DB.c QV.c -lm
+
+DBdump: DBdump.c DB.c DB.h QV.c QV.h
+	gcc $(CFLAGS) -o DBdump DBdump.c DB.c QV.c -lm
+
+DBstats: DBstats.c DB.c DB.h QV.c QV.h
+	gcc $(CFLAGS) -o DBstats DBstats.c DB.c QV.c -lm
+
+DBrm: DBrm.c DB.c DB.h QV.c QV.h
+	gcc $(CFLAGS) -o DBrm DBrm.c DB.c QV.c -lm
+
+simulator: simulator.c DB.c DB.h QV.c QV.h
+	gcc $(CFLAGS) -o simulator simulator.c DB.c QV.c -lm
+
+fasta2DAM: fasta2DAM.c DB.c DB.h QV.c QV.h
+	gcc $(CFLAGS) -o fasta2DAM fasta2DAM.c DB.c QV.c -lm
+
+DAM2fasta: DAM2fasta.c DB.c DB.h QV.c QV.h
+	gcc $(CFLAGS) -o DAM2fasta DAM2fasta.c DB.c QV.c -lm
+
+DBupgrade.Sep.25.2014: DBupgrade.Sep.25.2014.c DB.c DB.h QV.c QV.h
+	gcc $(CFLAGS) -o DBupgrade.Sep.25.2014 DBupgrade.Sep.25.2014.c DB.c QV.c -lm
+
+DBupgrade.Dec.31.2014: DBupgrade.Dec.31.2014.c DB.c DB.h QV.c QV.h
+	gcc $(CFLAGS) -o DBupgrade.Dec.31.2014 DBupgrade.Dec.31.2014.c DB.c QV.c -lm
+
+DUSTupgrade.Jan.1.2015: DUSTupgrade.Jan.1.2015.c DB.c DB.h QV.c QV.h
+	gcc $(CFLAGS) -o DUSTupgrade.Jan.1.2015 DUSTupgrade.Jan.1.2015.c DB.c QV.c -lm
+
+clean:
+	rm -f $(ALL)
+	rm -fr *.dSYM
+	rm -f DBupgrade.Sep.25.2014 DBupgrade.Dec.31.2014 DUSTupgrade.Jan.1.2015
+	rm -f dazz.db.tar.gz
+
+install:
+	cp $(ALL) ~/bin
+
+package:
+	make clean
+	tar -zcf dazz.db.tar.gz README Makefile *.h *.c

binary/centos6/thirdparty/DAZZ_DB/QV.h

@@ -0,0 +1,125 @@
+/************************************************************************************\
+*                                                                                    *
+* Copyright (c) 2014, Dr. Eugene W. Myers (EWM). All rights reserved.                *
+*                                                                                    *
+* Redistribution and use in source and binary forms, with or without modification,   *
+* are permitted provided that the following conditions are met:                      *
+*                                                                                    *
+*  · Redistributions of source code must retain the above copyright notice, this     *
+*    list of conditions and the following disclaimer.                                *
+*                                                                                    *
+*  · Redistributions in binary form must reproduce the above copyright notice, this  *
+*    list of conditions and the following disclaimer in the documentation and/or     *
+*    other materials provided with the distribution.                                 *
+*                                                                                    *
+*  · The name of EWM may not be used to endorse or promote products derived from     *
+*    this software without specific prior written permission.                        *
+*                                                                                    *
+* THIS SOFTWARE IS PROVIDED BY EWM ”AS IS” AND ANY EXPRESS OR IMPLIED WARRANTIES,    *
+* INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND       *
+* FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL EWM BE LIABLE   *
+* FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES *
+* (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS  *
+* OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY      *
+* THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING     *
+* NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN  *
+* IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.                                      *
+*                                                                                    *
+* For any issues regarding this software and its use, contact EWM at:                *
+*                                                                                    *
+*   Eugene W. Myers Jr.                                                              *
+*   Bautzner Str. 122e                                                               *
+*   01099 Dresden                                                                    *
+*   GERMANY                                                                          *
+*   Email: gene.myers@gmail.com                                                      *
+*                                                                                    *
+\************************************************************************************/
+
+/*******************************************************************************************
+ *
+ *  Compressor/decompressor for .quiv files: customized Huffman codes for each stream based on
+ *    the histogram of values occuring in a given file.  The two low complexity streams
+ *    (deletionQV and substitutionQV) use a Huffman coding of the run length of the prevelant
+ *    character.
+ *
+ *  Author:   Gene Myers
+ *  Date:     Jan 18, 2014
+ *  Modified: July 25, 2014
+ *
+ ********************************************************************************************/
+
+#ifndef _QV_COMPRESSOR
+
+#define _QV_COMPRESSOR
+
+  //  The defined constant INTERACTIVE (set in DB.h) determines whether an interactive or
+  //    batch version of the routines in this library are compiled.  In batch mode, routines
+  //    print an error message and exit.  In interactive mode, the routines place the error
+  //    message in EPLACE (also defined in DB.h) and return an error value, typically NULL
+  //    if the routine returns a pointer, and an unusual integer value if the routine returns
+  //    an integer.
+  //  Below when an error return is described, one should understand that this value is returned
+  //    only if the routine was compiled in INTERACTIVE mode.
+
+  //  A PacBio compression scheme
+
+typedef struct
+  { void    *delScheme;   //  Huffman scheme for deletion QVs
+    void    *insScheme;   //  Huffman scheme for insertion QVs
+    void    *mrgScheme;   //  Huffman scheme for merge QVs
+    void    *subScheme;   //  Huffman scheme for substitution QVs
+    void    *dRunScheme;  //  Huffman scheme for deletion run lengths (if delChar > 0)
+    void    *sRunScheme;  //  Huffman scheme for substitution run lengths (if subChar > 0)
+    int      delChar;     //  If > 0, run-encoded deletion value
+    int      subChar;     //  If > 0, run-encoded substitution value
+    int      flip;        //  Need to flip multi-byte integers
+    char    *prefix;      //  Header line prefix
+  } QVcoding;
+
+  // Read the next nlines of input, and QVentry returns a pointer to the first line if needed.
+  //   If end-of-input is encountered before any further input, -1 is returned.  If there is
+  //   an error than -2 is returned.  Otherwise the length of the line(s) read is returned.
+
+int       Read_Lines(FILE *input, int nlines);
+char     *QVentry();
+
+  // Read the .quiva file on input and record frequency statistics.  If there is an error
+  //  then 1 is returned, otherwise 0.
+
+int       QVcoding_Scan(FILE *input);
+
+  // Given QVcoding_Scan has been called at least once, create an encoding scheme based on
+  //   the accumulated statistics and return a pointer to it.  The returned encoding object
+  //   is *statically allocated within the routine.  If lossy is set then use a lossy scaling
+  //   for the insertion and merge streams.  If there is an error, then NULL is returned.
+
+QVcoding *Create_QVcoding(int lossy);
+
+  //  Read/write a coding scheme to input/output.  The encoding object returned by the reader
+  //    is *statically* allocated within the routine.  If an error occurs while reading then
+  //    NULL is returned.
+
+QVcoding *Read_QVcoding(FILE *input);
+void      Write_QVcoding(FILE *output, QVcoding *coding);
+
+  //  Free all the auxiliary storage associated with coding (but not the object itself!)
+
+void      Free_QVcoding(QVcoding *coding);
+
+  //  Assuming the file pointer is positioned just beyond an entry header line, read the
+  //    next set of 5 QV lines, compress them according to 'coding', and output.  If lossy
+  //    is set then the scheme is a lossy one.  A non-zero value is return only if an
+  //    error occured.
+
+int      Compress_Next_QVentry(FILE *input, FILE *output, QVcoding *coding, int lossy);
+
+  //  Assuming the input is position just beyond the compressed encoding of an entry header,
+  //    read the set of compressed encodings for the ensuing 5 QV vectors, decompress them,
+  //    and place their decompressed values into entry which is a 5 element array of character
+  //    pointers.  The parameter rlen computed from the preceeding header line, critically
+  //    provides the length of each of the 5 vectors.  A non-zero value is return only if an
+  //    error occured.
+
+int      Uncompress_Next_QVentry(FILE *input, char **entry, QVcoding *coding, int rlen);
+
+#endif // _QV_COMPRESSOR