New upstream version 1.0+git20190616.034f1ab (f34d525d) · Commits · Debian Med / dazzdb

Catrack.c

+270 −247

Original line number	Diff line number	Diff line
		@@ -22,13 +22,14 @@
		#define PATHSEP "/"
		#endif

		static char *Usage = "[-vfd] <path:db\|dam> <track:name>";
		static char *Usage = "[-vfd] <path:db\|dam> <track:name> ...";

		int main(int argc, char *argv[])
		{ char *prefix;
		FILE aout, dout;
		int nblocks;
		int nfiles;
		FILE aout, dout;
		int c;

		int VERBOSE;
		int FORCE;
		int DELETE;
		@@ -52,7 +53,7 @@ int main(int argc, char *argv[])
		FORCE = flags['f'];
		DELETE = flags['d'];

		if (argc != 3)
		if (argc < 3)
		{ fprintf(stderr,"Usage: %s %s\n",Prog_Name,Usage);
		fprintf(stderr,"\n");
		fprintf(stderr," -v: verbose\n");
		@@ -62,6 +63,8 @@ int main(int argc, char *argv[])
		}
		}

		// Open DB stub and get number of blocks

		{ char pwd, root;
		int i, plen, index, isdam;
		FILE *dstub;
		@@ -103,26 +106,13 @@ int main(int argc, char *argv[])
		free(dstub_name);
		free(pwd);
		free(root);

		aout = fopen(Catenate(prefix,argv[2],".","anno"),"r");
		if (aout != NULL && !FORCE)
		{ fprintf(stderr,"%s: Track file %s%s.anno already exists!\n",Prog_Name,prefix,argv[2]);
		exit (1);
		}

		dout = fopen(Catenate(prefix,argv[2],".","data"),"r");
		if (dout != NULL && !FORCE)
		{ fprintf(stderr,"%s: Track file %s%s.data already exists!\n",Prog_Name,prefix,argv[2]);
		exit (1);
		}
		// For each track do

		aout = Fopen(Catenate(prefix,argv[2],".","anno"),"w");
		if (aout == NULL)
		exit (1);
		dout = NULL;
		}

		{ int tracktot, tracksiz;
		for (c = 2; c < argc; c++)
		{ int nfiles;
		int tracktot, tracksiz;
		int64 trackoff;
		char data[1024];
		void *anno;
		@@ -131,6 +121,36 @@ int main(int argc, char *argv[])
		int nextra;
		int64 extail;

		// Open the output .anno for writing, and output header stub

		if (VERBOSE)
		{ fprintf(stderr,"\nConstructing %s%s:\n",prefix,argv[c]);
		fflush(stderr);
		}

		aout = fopen(Catenate(prefix,argv[c],".","anno"),"r");
		if (aout != NULL)
		{ if (!FORCE)
		{ fprintf(stderr,"%s: Track file %s%s.anno already exists!\n",Prog_Name,prefix,argv[c]);
		exit (1);
		}
		fclose(aout);
		}

		dout = fopen(Catenate(prefix,argv[c],".","data"),"r");
		if (dout != NULL)
		{ if (!FORCE)
		{ fprintf(stderr,"%s: Track file %s%s.data already exists!\n",Prog_Name,prefix,argv[c]);
		exit (1);
		}
		fclose(dout);
		}

		aout = Fopen(Catenate(prefix,argv[c],".","anno"),"w");
		if (aout == NULL)
		exit (1);
		dout = NULL;

		extra = NULL;
		anno = NULL;
		trackoff = 0;
		@@ -140,6 +160,8 @@ int main(int argc, char *argv[])
		if (fwrite(&tracksiz,sizeof(int),1,aout) != 1)
		SYSTEM_WRITE_ERROR

		// OPen and catenate in each block .anno and .data file

		nextra = 0;
		nfiles = 0;
		while (1)
		@@ -147,9 +169,9 @@ int main(int argc, char *argv[])
		char dfile_name, afile_name;
		int i, apos, size, esize, tracklen;

		afile_name = Strdup(Numbered_Suffix(prefix,nfiles+1,Catenate(".",argv[2],".","anno")),
		afile_name = Strdup(Numbered_Suffix(prefix,nfiles+1,Catenate(".",argv[c],".","anno")),
		"Allocating .anno file name");
		dfile_name = Strdup(Numbered_Suffix(prefix,nfiles+1,Catenate(".",argv[2],".","data")),
		dfile_name = Strdup(Numbered_Suffix(prefix,nfiles+1,Catenate(".",argv[c],".","data")),
		"Allocating .data file name");
		if (afile_name == NULL \|\| dfile_name == NULL)
		goto error;
		@@ -158,7 +180,7 @@ int main(int argc, char *argv[])
		afile = fopen(afile_name,"r");
		if (afile == NULL)
		break;
		dfile = fopen(Numbered_Suffix(prefix,nfiles+1,Catenate(".",argv[2],".","data")),"r");
		dfile = fopen(Numbered_Suffix(prefix,nfiles+1,Catenate(".",argv[c],".","data")),"r");
		if (dfile == NULL && errno != ENOENT)
		{ fprintf(stderr,"%s: The file %s is corrupted\n",Prog_Name,dfile_name);
		goto error;
		@@ -169,12 +191,12 @@ int main(int argc, char *argv[])
		lfile = afile;

		if (VERBOSE)
		{ fprintf(stderr,"Concatenating %s%d.%s ...\n",prefix,nfiles+1,argv[2]);
		{ fprintf(stderr," Concatenating %s%d.%s ...\n",prefix,nfiles+1,argv[c]);
		fflush(stderr);
		}

		FREAD(&tracklen,sizeof(int),1,afile)
		FREAD(&size,sizeof(int),1,afile)
		FFREAD(&tracklen,sizeof(int),1,afile)
		FFREAD(&size,sizeof(int),1,afile)
		if (size == 0)
		esize = 8;
		else
		@@ -183,7 +205,7 @@ int main(int argc, char *argv[])
		if (nfiles == 0)
		{ tracksiz = size;
		if (dfile != NULL)
		{ dout = Fopen(Catenate(prefix,argv[2],".","data"),"w");
		{ dout = Fopen(Catenate(prefix,argv[c],".","data"),"w");
		if (dout == NULL)
		goto error;
		}
		@@ -213,46 +235,46 @@ int main(int argc, char *argv[])
		}

		if (dfile != NULL)
		{ int64 dlen;
		{ int64 dlen, d;

		if (esize == 4)
		{ int anno4;

		for (i = 0; i < tracklen; i++)
		{ FREAD(&anno4,sizeof(int),1,afile)
		{ FFREAD(&anno4,sizeof(int),1,afile)
		anno4 += trackoff;
		FWRITE(&anno4,sizeof(int),1,aout)
		FFWRITE(&anno4,sizeof(int),1,aout)
		}
		FREAD(&anno4,sizeof(int),1,afile)
		FFREAD(&anno4,sizeof(int),1,afile)
		dlen = anno4;
		}
		else
		{ int64 anno8;

		for (i = 0; i < tracklen; i++)
		{ FREAD(&anno8,sizeof(int64),1,afile)
		{ FFREAD(&anno8,sizeof(int64),1,afile)
		anno8 += trackoff;
		FWRITE(&anno8,sizeof(int64),1,aout)
		FFWRITE(&anno8,sizeof(int64),1,aout)
		}
		FREAD(&anno8,sizeof(int64),1,afile)
		FFREAD(&anno8,sizeof(int64),1,afile)
		dlen = anno8;
		}
		trackoff += dlen;

		for (i = 1024; i < dlen; i += 1024)
		{ FREAD(data,1024,1,dfile)
		FWRITE(data,1024,1,dout)
		for (d = 1024; d < dlen; d += 1024)
		{ FFREAD(data,1024,1,dfile)
		FFWRITE(data,1024,1,dout)
		}
		i -= 1024;
		if (i < dlen)
		{ FREAD(data,dlen-i,1,dfile)
		FWRITE(data,dlen-i,1,dout)
		d -= 1024;
		if (d < dlen)
		{ FFREAD(data,dlen-d,1,dfile)
		FFWRITE(data,dlen-d,1,dout)
		}
		}
		else
		{ for (i = 0; i < tracklen; i++)
		{ FREAD(anno,esize,1,afile)
		FWRITE(anno,esize,1,aout)
		{ FFREAD(anno,esize,1,afile)
		FFWRITE(anno,esize,1,aout)
		}
		}

		@@ -307,7 +329,7 @@ int main(int argc, char *argv[])

		if (nfiles == 0)
		{ fprintf(stderr,"%s: Couldn't find first track block %s1.%s.anno\n",
		Prog_Name,prefix,argv[2]);
		Prog_Name,prefix,argv[c]);
		goto error;
		}
		else
		@@ -316,17 +338,17 @@ int main(int argc, char *argv[])
		if (dout != NULL)
		{ if (tracksiz == 4)
		{ int anno4 = trackoff;
		FWRITE(&anno4,sizeof(int),1,aout)
		FFWRITE(&anno4,sizeof(int),1,aout)
		}
		else
		{ int64 anno8 = trackoff;
		FWRITE(&anno8,sizeof(int64),1,aout)
		FFWRITE(&anno8,sizeof(int64),1,aout)
		}
		}

		if (nextra == 0)
		{ while (fread(&byte,1,1,lfile) == 1)
		FWRITE(&byte,1,1,aout)
		FFWRITE(&byte,1,1,aout)
		}
		else
		{ int i;
		@@ -336,9 +358,8 @@ int main(int argc, char *argv[])
		fclose(lfile);

		FSEEKO(aout,0,SEEK_SET)
		FWRITE(&tracktot,sizeof(int),1,aout)
		FWRITE(&tracksiz,sizeof(int),1,aout)
		}
		FFWRITE(&tracktot,sizeof(int),1,aout)
		FFWRITE(&tracksiz,sizeof(int),1,aout)
		}

		if (nfiles != nblocks)
		@@ -356,17 +377,19 @@ int main(int argc, char *argv[])
		char *name;

		for (i = 1; i <= nblocks ;i++)
		{ name = Numbered_Suffix(prefix,i,Catenate(".",argv[2],".","anno"));
		{ name = Numbered_Suffix(prefix,i,Catenate(".",argv[c],".","anno"));
		if (unlink(name) != 0)
		fprintf(stderr,"%s: [WARNING] Couldn't delete file %s\n",Prog_Name,name);
		if (dout != NULL)
		{ name = Numbered_Suffix(prefix,i,Catenate(".",argv[2],".","data"));
		{ name = Numbered_Suffix(prefix,i,Catenate(".",argv[c],".","data"));
		if (unlink(name) != 0)
		fprintf(stderr,"%s: [WARNING] Couldn't delete file %s\n",Prog_Name,name);
		}
		}
		}

		}

		free(prefix);
		exit (0);

		@@ -374,17 +397,17 @@ error:
		{ char *name;

		fclose(aout);
		name = Catenate(prefix,argv[2],".","anno");
		name = Catenate(prefix,argv[c],".","anno");
		if (unlink(name) != 0)
		fprintf(stderr,"%s: [WARNING] Couldn't delete file %s during abort\n",Prog_Name,name);
		if (dout != NULL)
		{ fclose(dout);
		name = Catenate(prefix,argv[2],".","data");
		name = Catenate(prefix,argv[c],".","data");
		if (unlink(name) != 0)
		fprintf(stderr,"%s: [WARNING] Couldn't delete file %s during abort\n",Prog_Name,name);
		}
		free(prefix);
		}

		free(prefix);
		exit (1);
		}

DB.c

+1303 −799

File changed.

Preview size limit exceeded, changes collapsed.

DB.h

+175 −81

File changed.

Preview size limit exceeded, changes collapsed.

DBa2b.c

0 → 100644

+108 −0

Original line number	Diff line number	Diff line
		#include <stdlib.h>
		#include <stdio.h>

		#include "DB.h"

		int main(int argc, char *argv[])
		{ char code, which;
		int64 total;
		int len, rno, mno, qual;
		int vec[4];
		char *buffer[256];
		char **mname;
		int **masks;

		(void) argv;

		if (argc > 1)
		{ fprintf(stderr,"Usage: DBa2b <(ascii) >(binary)\n");
		exit (1);
		}

		while (scanf(" %c",&code) == 1) // Header lines
		if (code == '@' \|\| code == '+')
		{ scanf(" %c",&which);
		fwrite(&code,sizeof(char),1,stdout);
		fwrite(&which,sizeof(char),1,stdout);
		if (which == 'T')
		{ scanf("%d %lld",&mno,&total);
		fwrite(&mno,sizeof(int),1,stdout);
		fwrite(&total,sizeof(int64),1,stdout);
		if (code == '@')
		{ masks[mno] = (int ) malloc(sizeof(int)2*total);
		scanf(" %d",&len);
		mname[mno] = (char ) malloc(sizeof(char)(len+1));
		scanf(" %s",mname[mno]);
		fwrite(&len,sizeof(int),1,stdout);
		fwrite(mname[mno],sizeof(char),len,stdout);
		}
		}
		else
		{ scanf(" %lld",&total);
		if (which == 'M')
		{ masks = (int *) malloc(sizeof(int )*total);
		mname = (char *) malloc(sizeof(char )*total);
		}
		else if (code == '@')
		buffer[(int) which] = malloc(total+1);
		fwrite(&total,sizeof(int64),1,stdout);
		}
		}
		else
		{ ungetc(code,stdin);
		break;
		}

		buffer['A'] = buffer['c'] = buffer['d'] =
		buffer['i'] = buffer['m'] = buffer['s'] = buffer['S'];

		while (scanf(" %c",&code) == 1) // For each data line do
		{ fwrite(&code,sizeof(char),1,stdout);
		switch (code)
		{ case 'R': // Read
		scanf(" %d",&rno);
		fwrite(&rno,sizeof(int),1,stdout);
		break;
		case 'Q': // Read
		scanf(" %d",&qual);
		fwrite(&qual,sizeof(int),1,stdout);
		break;
		case 'L': // Well, Pulse range
		scanf(" %d %d %d",vec,vec+1,vec+2);
		fwrite(vec,sizeof(int),3,stdout);
		break;
		case 'N': // SNR values
		scanf(" %d %d %d %d",vec,vec+1,vec+2,vec+3);
		fwrite(vec,sizeof(int),4,stdout);
		break;
		case 'S': case 'A': case 'c': // DNA strings (2-bit compressible)
		scanf(" %d",&len);
		scanf(" %s",buffer[(int) code]);
		if (code == 'A')
		Number_Arrow(buffer[(int) code]);
		else
		Number_Read(buffer[(int) code]);
		Compress_Read(len,buffer[(int) code]);
		fwrite(&len,sizeof(int),1,stdout);
		fwrite(buffer[(int) code],sizeof(char),COMPRESSED_LEN(len),stdout);
		break;
		case 'H': case 'I': case 'F': // All other string fields
		case 'd': case 'i':
		case 'm': case 's':
		scanf(" %d",&len);
		scanf(" %s",buffer[(int) code]);
		fwrite(&len,sizeof(int),1,stdout);
		fwrite(buffer[(int) code],sizeof(char),len,stdout);
		break;
		case 'T': // Mask
		scanf("%d %d",&mno,&len);
		for (int i = 0; i < len; i++)
		scanf(" %d %d",masks[mno]+2i,masks[mno]+2i+1);
		fwrite(&mno,sizeof(int),1,stdout);
		fwrite(&len,sizeof(int),1,stdout);
		fwrite(masks[mno],sizeof(int),2*len,stdout);
		}
		}

		exit (0);
		}

DBb2a.c

0 → 100644

+109 −0

Original line number	Diff line number	Diff line
		#include <stdlib.h>
		#include <stdio.h>

		#include "DB.h"

		int main(int argc, char *argv[])
		{ char code, which;
		int64 total;
		int len, rno, mno, qual;
		int vec[4];
		char *buffer[256];
		char **mname;
		int **masks;

		(void) argv;

		if (argc > 1)
		{ fprintf(stderr,"Usage: DBb2a <(binary) >(ascii)\n");
		exit (1);
		}

		if (fread(&code,sizeof(char),1,stdin) == 0)
		code = 0;

		while (code == '@' \|\| code == '+')
		{ fread(&which,sizeof(char),1,stdin);
		printf("%c %c",code,which);
		if (which == 'T')
		{ fread(&mno,sizeof(int),1,stdin);
		fread(&total,sizeof(int64),1,stdin);
		printf("%d %lld",mno,total);
		if (code == '@')
		{ masks[mno] = (int ) malloc(sizeof(int)2*total);
		fread(&len,sizeof(int),1,stdin);
		mname[mno] = (char ) malloc(sizeof(char)(len+1));
		fread(mname[mno],sizeof(char),len,stdin);
		printf(" %d %.*s",len,len,mname[mno]);
		}
		printf("\n");
		}
		else
		{ fread(&total,sizeof(int64),1,stdin);
		if (which == 'M')
		{ masks = (int *) malloc(sizeof(int )*total);
		mname = (char *) malloc(sizeof(char )*total);
		}
		else if (code == '@')
		buffer[(int) which] = malloc(total+1);
		printf(" %lld\n",total);
		}

		if (fread(&code,sizeof(char),1,stdin) == 0)
		code = 0;
		}

		buffer['A'] = buffer['c'] = buffer['d'] =
		buffer['i'] = buffer['m'] = buffer['s'] = buffer['S'];

		while (code != 0) // For each data line do
		{ switch (code)
		{ case 'R': // Read
		fread(&rno,sizeof(int),1,stdin);
		printf("R %d\n",rno);
		break;
		case 'Q': // Qual Value
		fread(&qual,sizeof(int),1,stdin);
		printf("Q %d\n",qual);
		break;
		case 'L': // Well, Pulse range
		fread(vec,sizeof(int),3,stdin);
		printf("L %d %d %d\n",vec[0],vec[1],vec[2]);
		break;
		case 'N': // SNR values
		fread(vec,sizeof(int),4,stdin);
		printf("N %d %d %d %d\n",vec[0],vec[1],vec[2],vec[3]);
		break;
		case 'S': case 'A': case 'c': // DNA strings (2-bit compressible)
		fread(&len,sizeof(int),1,stdin);
		fread(buffer[(int) code],sizeof(char),COMPRESSED_LEN(len),stdin);
		Uncompress_Read(len,buffer[(int) code]);
		if (code == 'A')
		Letter_Arrow(buffer[(int) code]);
		else
		Lower_Read(buffer[(int) code]);
		printf("%c %d %.*s\n",code,len,len,buffer[(int) code]);
		break;
		case 'H': case 'I': case 'F': // All other string fields
		case 'd': case 'i':
		case 'm': case 's':
		fread(&len,sizeof(int),1,stdin);
		fread(buffer[(int) code],sizeof(char),len,stdin);
		printf("%c %d %.*s\n",code,len,len,buffer[(int) code]);
		break;
		case 'T': // Mask
		fread(&mno,sizeof(int),1,stdin);
		fread(&len,sizeof(int),1,stdin);
		fread(masks[mno],sizeof(int),2*len,stdin);
		printf("T%d %d",mno,len);
		for (int i = 0; i < len; i++)
		printf(" %d %d",masks[mno][2i],masks[mno][2i+1]);
		printf("\n");
		}

		if (fread(&code,sizeof(char),1,stdin) == 0)
		code = 0;
		}

		exit (0);
		}