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/************************************************************************************\
* *
* 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 for .quiv files, customized Huffman codes for each stream based on the
* histogram of values occuring in the 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
*
********************************************************************************************/
#include <stdlib.h>
#include <stdio.h>
#include <string.h>
#include <math.h>
#include <unistd.h>
#include "DB.h"
static char *Usage = "[-vkl] <path:quiva> ...";
int main(int argc, char* argv[])
{ int VERBOSE;
int KEEP;
int LOSSY;
{ int i, j, k;
int flags[128];
ARG_INIT("dexqv")
j = 1;
for (i = 1; i < argc; i++)
if (argv[i][0] == '-')
{ ARG_FLAGS("vkl") }
else
argv[j++] = argv[i];
argc = j;
VERBOSE = flags['v'];
KEEP = flags['k'];
LOSSY = flags['l'];
if (argc == 1)
{ fprintf(stderr,"Usage: %s %s\n",Prog_Name,Usage);
exit (1);
}
}
// For each .quiva file to be compressed:
{ int i;
for (i = 1; i < argc; i++)
{ char *pwd, *root;
FILE *input, *output;
QVcoding *coding;
pwd = PathTo(argv[i]);
root = Root(argv[i],".quiva");
input = Fopen(Catenate(pwd,"/",root,".quiva"),"r");
if (input == NULL)
exit (1);
output = Fopen(Catenate(pwd,"/",root,".dexqv"),"w");
if (output == NULL)
exit (1);
if (VERBOSE)
{ fprintf(stderr,"Processing '%s' ...\n",root);
fflush(stderr);
}
// Scan the file collecting statistics for Huffman schemes
QVcoding_Scan(input);
// Create and output the encoding schemes
coding = Create_QVcoding(LOSSY);
{ char *slash, *read; // Get header line prefix from first line
rewind (input);
Read_Lines(input,1);
read = QVentry();
slash = index(read+1,'/');
coding->prefix = (char *) malloc((slash-read)+1);
if (coding->prefix == NULL)
{ fprintf(stderr,"%s: Out of memory (Allocating header prefix)\n",Prog_Name);
exit (1);
}
*slash = '\0';
strcpy(coding->prefix,read);
*slash = '/';
}
Write_QVcoding(output,coding);
// For each entry do
{ int lwell;
rewind (input);
lwell = 0;
while (Read_Lines(input,1) > 0)
{ int well, beg, end, qv;
char *slash;
uint16 half;
uint8 byte;
// Interpret the header, encode and write out the fields
slash = index(QVentry(),'/');
sscanf(slash+1,"%d/%d_%d RQ=0.%d\n",&well,&beg,&end,&qv);
while (well - lwell >= 255)
{ byte = 0xff;
fwrite(&byte,1,1,output);
lwell += 255;
}
byte = (uint8) (well-lwell);
fwrite(&byte,1,1,output);
lwell = well;
half = (uint16) beg;
fwrite(&half,sizeof(uint16),1,output);
half = (uint16) end;
fwrite(&half,sizeof(uint16),1,output);
half = (uint16) qv;
fwrite(&half,sizeof(uint16),1,output);
Compress_Next_QVentry(input,output,coding,LOSSY);
}
}
// Clean up for the next file
Free_QVcoding(coding);
fclose(input);
fclose(output);
if (!KEEP)
unlink(Catenate(pwd,"/",root,".quiva"));
free(root);
free(pwd);
if (VERBOSE)
{ fprintf(stderr,"Done\n");
fflush(stderr);
}
}
}
free(QVentry());
exit (0);
}
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