Catrack.c

@@ -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;
@@ -103,268 +106,288 @@ 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);
-      }
+  //  For each track do
 
-    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 (c = 2; c < argc; c++)
+    { int   nfiles;
+      int   tracktot, tracksiz;
+      int64 trackoff;
+      char  data[1024];
+      void *anno;
+      FILE *lfile = NULL;
+      DAZZ_EXTRA *extra;
+      int         nextra;
+      int64       extail;
 
-    aout = Fopen(Catenate(prefix,argv[2],".","anno"),"w");
-    if (aout == NULL)
-      exit (1);
-    dout = NULL;
-  }
- 
-  { int   tracktot, tracksiz;
-    int64 trackoff;
-    char  data[1024];
-    void *anno;
-    FILE *lfile = NULL;
-    DAZZ_EXTRA *extra;
-    int         nextra;
-    int64       extail;
-
-    extra    = NULL;
-    anno     = NULL;
-    trackoff = 0;
-    tracktot = tracksiz = 0;
-    if (fwrite(&tracktot,sizeof(int),1,aout) != 1)
-      SYSTEM_WRITE_ERROR
-    if (fwrite(&tracksiz,sizeof(int),1,aout) != 1)
-      SYSTEM_WRITE_ERROR
-
-    nextra = 0;
-    nfiles = 0;
-    while (1)
-      { FILE *dfile, *afile;
-        char *dfile_name, *afile_name;
-        int   i, apos, size, esize, tracklen;
-
-        afile_name = Strdup(Numbered_Suffix(prefix,nfiles+1,Catenate(".",argv[2],".","anno")),
-                            "Allocating .anno file name");
-        dfile_name = Strdup(Numbered_Suffix(prefix,nfiles+1,Catenate(".",argv[2],".","data")),
-                            "Allocating .data file name");
-        if (afile_name == NULL || dfile_name == NULL)
-          goto error;
-          
-
-        afile = fopen(afile_name,"r");
-        if (afile == NULL)
-          break;
-        dfile = fopen(Numbered_Suffix(prefix,nfiles+1,Catenate(".",argv[2],".","data")),"r");
-        if (dfile == NULL && errno != ENOENT)
-          { fprintf(stderr,"%s: The file %s is corrupted\n",Prog_Name,dfile_name);
-            goto error;
-          }
+      //  Open the output .anno for writing, and output header stub
 
-        if (nfiles > 0)
-          fclose(lfile);
-        lfile = afile;
+      if (VERBOSE)
+        { fprintf(stderr,"\nConstructing %s%s:\n",prefix,argv[c]);
+          fflush(stderr);
+        }
 
-        if (VERBOSE)
-          { fprintf(stderr,"Concatenating %s%d.%s ...\n",prefix,nfiles+1,argv[2]);
-            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;
+      tracktot = tracksiz = 0;
+      if (fwrite(&tracktot,sizeof(int),1,aout) != 1)
+        SYSTEM_WRITE_ERROR
+      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)
+        { FILE *dfile, *afile;
+          char *dfile_name, *afile_name;
+          int   i, apos, size, esize, tracklen;
   
-        FREAD(&tracklen,sizeof(int),1,afile)
-        FREAD(&size,sizeof(int),1,afile)
-        if (size == 0)
-          esize = 8;
-        else
-          esize = size;
-
-        if (nfiles == 0)
-          { tracksiz = size;
-            if (dfile != NULL)
-              { dout = Fopen(Catenate(prefix,argv[2],".","data"),"w");
-                if (dout == NULL)
-                  goto error;
-              }
-            else
-              { anno = Malloc(esize,"Allocating annotation record");
-                if (anno == NULL)
-                  goto error;
-              }
-          }
-        else
-          { int escape = 1;
-            if (tracksiz != size)
-              { fprintf(stderr,"%s: Track block %d does not have the same annotation size (%d)",
-                               Prog_Name,nfiles+1,size);
-                fprintf(stderr," as previous blocks (%d)\n",tracksiz);
-              }
-            else if (dfile == NULL && dout != NULL)
-              fprintf(stderr,"%s: Track block %d does not have data but previous blocks do\n",
-                             Prog_Name,nfiles+1);
-            else if (dfile != NULL && dout == NULL)
-              fprintf(stderr,"%s: Track block %d has data but previous blocks do not\n",
-                             Prog_Name,nfiles+1);
-            else
-               escape = 0;
-            if (escape)
+          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[c],".","data")),
+                              "Allocating .data file name");
+          if (afile_name == NULL || dfile_name == NULL)
+            goto error;
+            
+  
+          afile = fopen(afile_name,"r");
+          if (afile == NULL)
+            break;
+          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;
-          }
+            }
   
-        if (dfile != NULL)
-          { int64 dlen;
-
-            if (esize == 4)
-              { int anno4;
+          if (nfiles > 0)
+            fclose(lfile);
+          lfile = afile;
   
-                for (i = 0; i < tracklen; i++)
-                  { FREAD(&anno4,sizeof(int),1,afile)
-                    anno4 += trackoff;
-                    FWRITE(&anno4,sizeof(int),1,aout)
-                  }
-                FREAD(&anno4,sizeof(int),1,afile)
-                dlen = anno4;
-              }
-            else
-              { int64 anno8;
+          if (VERBOSE)
+            { fprintf(stderr,"  Concatenating %s%d.%s ...\n",prefix,nfiles+1,argv[c]);
+              fflush(stderr);
+            }
+    
+          FFREAD(&tracklen,sizeof(int),1,afile)
+          FFREAD(&size,sizeof(int),1,afile)
+          if (size == 0)
+            esize = 8;
+          else
+            esize = size;
   
-                for (i = 0; i < tracklen; i++)
-                  { FREAD(&anno8,sizeof(int64),1,afile)
-                    anno8 += trackoff;
-                    FWRITE(&anno8,sizeof(int64),1,aout)
-                  }
-                FREAD(&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)
-              }
-            i -= 1024;
-            if (i < dlen)
-              { FREAD(data,dlen-i,1,dfile)
-                FWRITE(data,dlen-i,1,dout)
-              }
-          }
-        else
-          { for (i = 0; i < tracklen; i++)
-              { FREAD(anno,esize,1,afile)
-                FWRITE(anno,esize,1,aout)
-              }
-          }
-
-        FSEEKO(afile,0,SEEK_END)
-        FTELLO(apos,afile)
-        if (dfile != NULL)
-          extail = apos - (esize*(tracklen+1) + 2*sizeof(int)); 
-        else
-          extail = apos - (esize*tracklen + 2*sizeof(int)); 
-        FSEEKO(afile,-extail,SEEK_END)
-
-        if (extail >= 20)
-          { if (nfiles == 0)
-              { nextra = 0;
-                while (1)
-                  if (Read_Extra(afile,afile_name,NULL))
-                    break;
-                  else
-                    nextra += 1;
-
-                extra = (DAZZ_EXTRA *) Malloc(sizeof(DAZZ_EXTRA)*(nextra+1),"Allocating extras");
-                if (extra == NULL)
-                  goto error;
-                FSEEKO(afile,-extail,SEEK_END)
-
-                for (i = 0; i < nextra; i++)
-                  { extra[i].nelem = 0;
-                    Read_Extra(afile,afile_name,extra+i);
-                  }
-              }
-
-            else
-              { for (i = 0; i < nextra; i++)
-                  if (Read_Extra(afile,afile_name,extra+i))
-                    { fprintf(stderr,"%s: File %s has fewer extras than previous .anno files\n",
-                                     Prog_Name,afile_name);
-                      goto error;
+          if (nfiles == 0)
+            { tracksiz = size;
+              if (dfile != NULL)
+                { dout = Fopen(Catenate(prefix,argv[c],".","data"),"w");
+                  if (dout == NULL)
+                    goto error;
+                }
+              else
+                { anno = Malloc(esize,"Allocating annotation record");
+                  if (anno == NULL)
+                    goto error;
+                }
+            }
+          else
+            { int escape = 1;
+              if (tracksiz != size)
+                { fprintf(stderr,"%s: Track block %d does not have the same annotation size (%d)",
+                                 Prog_Name,nfiles+1,size);
+                  fprintf(stderr," as previous blocks (%d)\n",tracksiz);
+                }
+              else if (dfile == NULL && dout != NULL)
+                fprintf(stderr,"%s: Track block %d does not have data but previous blocks do\n",
+                               Prog_Name,nfiles+1);
+              else if (dfile != NULL && dout == NULL)
+                fprintf(stderr,"%s: Track block %d has data but previous blocks do not\n",
+                               Prog_Name,nfiles+1);
+              else
+                 escape = 0;
+              if (escape)
+                goto error;
+            }
+    
+          if (dfile != NULL)
+            { int64 dlen, d;
+  
+              if (esize == 4)
+                { int anno4;
+    
+                  for (i = 0; i < tracklen; i++)
+                    { FFREAD(&anno4,sizeof(int),1,afile)
+                      anno4 += trackoff;
+                      FFWRITE(&anno4,sizeof(int),1,aout)
+                    }
+                  FFREAD(&anno4,sizeof(int),1,afile)
+                  dlen = anno4;
+                }
+              else
+                { int64 anno8;
+    
+                  for (i = 0; i < tracklen; i++)
+                    { FFREAD(&anno8,sizeof(int64),1,afile)
+                      anno8 += trackoff;
+                      FFWRITE(&anno8,sizeof(int64),1,aout)
                     }
-                if (Read_Extra(afile,afile_name,extra+nextra) == 0)
-                  { fprintf(stderr,"%s: File %s has more extras than previous .anno files\n",
-                                   Prog_Name,afile_name);
+                  FFREAD(&anno8,sizeof(int64),1,afile)
+                  dlen = anno8;
+                }
+              trackoff += dlen;
+
+              for (d = 1024; d < dlen; d += 1024)
+                { FFREAD(data,1024,1,dfile)
+                  FFWRITE(data,1024,1,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++)
+                { FFREAD(anno,esize,1,afile)
+                  FFWRITE(anno,esize,1,aout)
+                }
+            }
+  
+          FSEEKO(afile,0,SEEK_END)
+          FTELLO(apos,afile)
+          if (dfile != NULL)
+            extail = apos - (esize*(tracklen+1) + 2*sizeof(int)); 
+          else
+            extail = apos - (esize*tracklen + 2*sizeof(int)); 
+          FSEEKO(afile,-extail,SEEK_END)
+
+          if (extail >= 20)
+            { if (nfiles == 0)
+                { nextra = 0;
+                  while (1)
+                    if (Read_Extra(afile,afile_name,NULL))
+                      break;
+                    else
+                      nextra += 1;
+  
+                  extra = (DAZZ_EXTRA *) Malloc(sizeof(DAZZ_EXTRA)*(nextra+1),"Allocating extras");
+                  if (extra == NULL)
                     goto error;
-                  }
-              }
-          }
+                  FSEEKO(afile,-extail,SEEK_END)
   
-        tracktot += tracklen;
-        nfiles   += 1;
-        if (dfile != NULL)
-          fclose(dfile);
-      }
+                  for (i = 0; i < nextra; i++)
+                    { extra[i].nelem = 0;
+                      Read_Extra(afile,afile_name,extra+i);
+                    }
+                }
   
-    if (nfiles == 0)
-      { fprintf(stderr,"%s: Couldn't find first track block %s1.%s.anno\n",
-                       Prog_Name,prefix,argv[2]);
-        goto error;
-      }
-    else
-      { char *byte;
-
-        if (dout != NULL)
-          { if (tracksiz == 4)
-              { int anno4 = trackoff;
-                FWRITE(&anno4,sizeof(int),1,aout)
-              }
-            else
-              { int64 anno8 = trackoff;
-                FWRITE(&anno8,sizeof(int64),1,aout)
-              }
-          }
+              else
+                { for (i = 0; i < nextra; i++)
+                    if (Read_Extra(afile,afile_name,extra+i))
+                      { fprintf(stderr,"%s: File %s has fewer extras than previous .anno files\n",
+                                       Prog_Name,afile_name);
+                        goto error;
+                      }
+                  if (Read_Extra(afile,afile_name,extra+nextra) == 0)
+                    { fprintf(stderr,"%s: File %s has more extras than previous .anno files\n",
+                                     Prog_Name,afile_name);
+                      goto error;
+                    }
+                }
+            }
+    
+          tracktot += tracklen;
+          nfiles   += 1;
+          if (dfile != NULL)
+            fclose(dfile);
+        }
 
-        if (nextra == 0)
-          { while (fread(&byte,1,1,lfile) == 1)
-              FWRITE(&byte,1,1,aout)
-          }
-        else
-          { int i;
-            for (i = 0; i < nextra; i++)
-              Write_Extra(aout,extra+i);
-          }
-        fclose(lfile);
+      if (nfiles == 0)
+        { fprintf(stderr,"%s: Couldn't find first track block %s1.%s.anno\n",
+                         Prog_Name,prefix,argv[c]);
+          goto error;
+        }
+      else
+        { char *byte;
 
-        FSEEKO(aout,0,SEEK_SET)
-        FWRITE(&tracktot,sizeof(int),1,aout)
-        FWRITE(&tracksiz,sizeof(int),1,aout)
-      }
-  }
+          if (dout != NULL)
+            { if (tracksiz == 4)
+                { int anno4 = trackoff;
+                  FFWRITE(&anno4,sizeof(int),1,aout)
+                }
+              else
+                { int64 anno8 = trackoff;
+                  FFWRITE(&anno8,sizeof(int64),1,aout)
+                }
+            }
+  
+          if (nextra == 0)
+            { while (fread(&byte,1,1,lfile) == 1)
+                FFWRITE(&byte,1,1,aout)
+            }
+          else
+            { int i;
+              for (i = 0; i < nextra; i++)
+                Write_Extra(aout,extra+i);
+            }
+          fclose(lfile);
 
-  if (nfiles != nblocks)
-    { fprintf(stderr,"%s: Did not catenate all tracks of DB (nfiles %d != nblocks %d)\n",
-	             Prog_Name, nfiles, nblocks);
-      goto error;
-    }
+          FSEEKO(aout,0,SEEK_SET)
+          FFWRITE(&tracktot,sizeof(int),1,aout)
+          FFWRITE(&tracksiz,sizeof(int),1,aout)
+        }
+
+      if (nfiles != nblocks)
+        { fprintf(stderr,"%s: Did not catenate all tracks of DB (nfiles %d != nblocks %d)\n",
+	                 Prog_Name, nfiles, nblocks);
+          goto error;
+        }
   
-  FCLOSE(aout);
-  if (dout != NULL)
-    FCLOSE(dout);
-
-  if (DELETE)
-    { int   i;
-      char *name;
-
-      for (i = 1; i <= nblocks ;i++)
-        { name = Numbered_Suffix(prefix,i,Catenate(".",argv[2],".","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"));
+      FCLOSE(aout);
+      if (dout != NULL)
+        FCLOSE(dout);
+
+      if (DELETE)
+        { int   i;
+          char *name;
+
+          for (i = 1; i <= nblocks ;i++)
+            { 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[c],".","data"));
+                  if (unlink(name) != 0)
+                    fprintf(stderr,"%s: [WARNING] Couldn't delete file %s\n",Prog_Name,name);
+                }
             }
         }
+    
     }
 
   free(prefix);
@@ -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);
 }

DBa2b.c

+#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]+2*i,masks[mno]+2*i+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

+#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][2*i],masks[mno][2*i+1]);
+          printf("\n");
+      }
+
+      if (fread(&code,sizeof(char),1,stdin) == 0)
+       code = 0;
+    }
+
+  exit (0);
+}

DBdust.c

@@ -133,11 +133,11 @@ int main(int argc, char *argv[])
         dfile = Fopen(Catenate(pwd,PATHSEP,root,".dust.data"),"w");
         if (dfile == NULL || afile == NULL)
           exit (1);
-        FWRITE(&(db->nreads),sizeof(int),1,afile)
-        FWRITE(&size,sizeof(int),1,afile)
+        FFWRITE(&(db->nreads),sizeof(int),1,afile)
+        FFWRITE(&size,sizeof(int),1,afile)
         nreads = 0;
         indx = 0;
-        FWRITE(&indx,sizeof(int64),1,afile)
+        FFWRITE(&indx,sizeof(int64),1,afile)
       }
     else
       { dfile = Fopen(Catenate(pwd,PATHSEP,root,".dust.data"),"r+");
@@ -151,8 +151,8 @@ int main(int argc, char *argv[])
             exit(0);
           }
         FSEEKO(afile,0,SEEK_SET)
-        FWRITE(&(db->nreads),sizeof(int),1,afile)
-        FWRITE(&size,sizeof(int),1,afile)
+        FFWRITE(&(db->nreads),sizeof(int),1,afile)
+        FFWRITE(&size,sizeof(int),1,afile)
         FSEEKO(afile,0,SEEK_END)
         FSEEKO(dfile,0,SEEK_END)
         FTELLO(indx,dfile)
@@ -435,8 +435,8 @@ int main(int argc, char *argv[])
               }
           mtop  = mask + ntop;
           indx += ntop*sizeof(int);
-          FWRITE(&indx,sizeof(int64),1,afile)
-          FWRITE(mask1,sizeof(int),ntop,dfile)
+          FFWRITE(&indx,sizeof(int64),1,afile)
+          FFWRITE(mask1,sizeof(int),ntop,dfile)
         }
 
 #ifdef DEBUG

DBshow.c

@@ -226,14 +226,20 @@ int main(int argc, char *argv[])
       }
   }
 
-  //  Load QVs if requested
+  //  Load QVs or Arrows if requested
 
   if (DOQVS)
-    { if (Load_QVs(db) < 0)
+    { if (Open_QVs(db) < 0)
         { fprintf(stderr,"%s: QVs requested, but no .qvs for data base\n",Prog_Name);
           exit (1);
         }
     }
+  if (DOARR)
+    { if (Open_Arrow(db) < 0)
+        { fprintf(stderr,"%s: Arrow requested, but no .arr for data base\n",Prog_Name);
+          exit (1);
+        }
+    }
 
   //  Check tracks and load tracks for untrimmed DB
 
@@ -248,7 +254,7 @@ int main(int argc, char *argv[])
         else if (kind != MASK_TRACK)
           printf("%s: Warning: %s track is not a mask track.\n",Prog_Name,MASK[i]);
         else if (status == 0)
-          Load_Track(db,MASK[i]);
+          Open_Track(db,MASK[i]);
         else if (status == 1 && !TRIM)
           printf("%s: Warning: %s track is for a trimmed db but -u is set.\n",Prog_Name,MASK[i]);
       }
@@ -336,10 +342,8 @@ int main(int argc, char *argv[])
 
       for (i = 0; i < MTOP; i++)
         { status = Check_Track(db,MASK[i],&kind);
-          if (status < 0)
-            continue;
-          else if (status == 1 && kind == MASK_TRACK)
-            Load_Track(db,MASK[i]);
+          if (status == 1 && kind == MASK_TRACK)
+            Open_Track(db,MASK[i]);
         }
     }
 
@@ -432,26 +436,35 @@ int main(int argc, char *argv[])
   //    range pairs in pts[0..reps) and according to the display options.
 
   { DAZZ_READ  *reads;
-    DAZZ_TRACK *first;
+    DAZZ_TRACK *first, *track;
     char       *read, *arrow, **entry;
+    int        *data[MTOP];
     int         c, b, e, i;
     int         hilight, substr;
     int         map;
     int       (*iscase)(int);
 
-    read  = New_Read_Buffer(db);
+    read = New_Read_Buffer(db);
+
     if (DOQVS)
       { entry = New_QV_Buffer(db);
+        arrow = NULL;
+        first = db->tracks->next;
+      }
+    else if (DOARR)
+      { entry = NULL;
+        arrow = New_Read_Buffer(db);
         first = db->tracks->next;
       }
     else
       { entry = NULL;
+        arrow = NULL;
         first = db->tracks;
       }
-    if (DOARR)
-      arrow = New_Read_Buffer(db);
-    else
-      arrow = NULL;
+
+    c = 0;
+    for (track = first; track != NULL; track = track->next)
+      data[c++] = (int *) New_Track_Buffer(track);
 
     if (UPPER == 1)
       { hilight = 'A'-'a';
@@ -491,7 +504,6 @@ int main(int argc, char *argv[])
             int         flags, qv;
             float       snr[4];
             DAZZ_READ  *r;
-            DAZZ_TRACK *track;
 
             r   = reads + i;
             len = r->rlen;
@@ -549,32 +561,30 @@ int main(int argc, char *argv[])
             if (DOARR)
               Load_Arrow(db,i,arrow,1);
 
-            for (track = first; track != NULL; track = track->next)
-              { int64 *anno;
-                int   *data;
-                int64  s, f, j;
-                int    bd, ed, m;
-
-                anno = (int64 *) track->anno;
-                data = (int *) track->data;
-
-                s = (anno[i] >> 2);
-                f = (anno[i+1] >> 2);
-                if (s < f)
-                  { for (j = s; j < f; j += 2)
-                      { bd = data[j];
-                        ed = data[j+1];
-                        if (DOSEQ)
-                          for (m = bd; m < ed; m++)
-                            if (iscase(read[m]))
-                              read[m] = (char) (read[m] + hilight);
-                        if (j == s)
-                          PRINTF("> %s:",track->name)
-                        PRINTF(" [%d,%d]",bd,ed)
-                      }
-                    PRINTF("\n")
-                  }
-              }
+            { int t;
+
+              for (t = 0, track = first; track != NULL; track = track->next, t += 1)
+                { int   *d;
+                  int64  j, v;
+                  int    bd, ed, m;
+
+                  d = data[t];
+                  v = (Load_Track_Data(track,i,d) >> 2);
+                  if (v > 0)
+                    { PRINTF("> %s:",track->name)
+                      for (j = 0; j < v; j += 2)
+                        { bd = d[j];
+                          ed = d[j+1];
+                          if (DOSEQ)
+                            for (m = bd; m < ed; m++)
+                              if (iscase(read[m]))
+                                read[m] = (char) (read[m] + hilight);
+                          PRINTF(" [%d,%d]",bd,ed)
+                        }
+                      PRINTF("\n")
+                    }
+                }
+            }
 
             if (QUIVA)
               { int k;

DBsplit.c

@@ -158,7 +158,7 @@ int main(int argc, char *argv[])
     for (i = 0; i < nfiles; i++)
       FGETS(buffer,2*MAX_NAME+100,dbfile)
 
-    FREAD(&dbs,sizeof(DAZZ_DB),1,ixfile)
+    FFREAD(&dbs,sizeof(DAZZ_DB),1,ixfile)
 
     if (dbs.cutoff >= 0 && !FORCE)
       { printf("You are about to overwrite the current partition settings.  This\n");
@@ -286,9 +286,9 @@ int main(int argc, char *argv[])
       dbs.allarr &= ~DB_ALL;
     dbs.treads = treads;
     FSEEKO(ixfile,0,SEEK_SET)
-    FWRITE(&dbs,sizeof(DAZZ_DB),1,ixfile)
+    FFWRITE(&dbs,sizeof(DAZZ_DB),1,ixfile)
     if (SELECT >= 0)
-      FWRITE(reads,sizeof(DAZZ_READ),nreads,ixfile)
+      FFWRITE(reads,sizeof(DAZZ_READ),nreads,ixfile)
   }
 
   FCLOSE(ixfile)

DBstats.c

@@ -105,7 +105,7 @@ int main(int argc, char *argv[])
         else if (kind != MASK_TRACK)
           fprintf(stderr,"%s: Warning: %s track is not a mask track.\n",Prog_Name,MASK[i]);
         else if (status == 0)
-          Load_Track(db,MASK[i]);
+          Open_Track(db,MASK[i]);
         else if (status == 1 && !TRIM)
           fprintf(stderr,"%s: Warning: %s track is for a trimmed db but -u is set.\n",
                          Prog_Name,MASK[i]);
@@ -124,7 +124,7 @@ int main(int argc, char *argv[])
             if (status < 0)
               continue;
             else if (status == 1)
-              Load_Track(db,MASK[i]);
+              Open_Track(db,MASK[i]);
           }
       }
   }
@@ -267,12 +267,17 @@ int main(int argc, char *argv[])
     DAZZ_TRACK *track;
 
     for (track = db->tracks; track != NULL; track = track->next)
-      { char  *data = track->data;
-        int64 *anno = (int64 *) track->anno;
+      { char  *data;
+        int64 *anno;
         int   *idata, *edata;
         int64  ave, dev, btot;
         int    k, rlen, cum;
 
+        Load_All_Track_Data(track);
+
+        data = track->data;
+        anno = (int64 *) track->anno;
+
         totlen = 0;
         numint = 0;
         maxlen = 0;
@@ -341,6 +346,8 @@ int main(int argc, char *argv[])
               }
           }
         printf("\n");
+
+        Close_Track(db,track);
       }
   }
 

DBtrim.c

@@ -139,7 +139,7 @@ int main(int argc, char *argv[])
     for (i = 0; i < nfiles; i++)
       FGETS(buffer,2*MAX_NAME+100,dbfile)
 
-    FREAD(&dbs,sizeof(DAZZ_DB),1,ixfile)
+    FFREAD(&dbs,sizeof(DAZZ_DB),1,ixfile)
 
     if (dbs.cutoff >= 0)
       { if (!FORCE)
@@ -248,9 +248,9 @@ int main(int argc, char *argv[])
       dbs.allarr &= ~DB_ALL;
     dbs.treads = t;
     FSEEKO(ixfile,0,SEEK_SET)
-    FWRITE(&dbs,sizeof(DAZZ_DB),1,ixfile)
+    FFWRITE(&dbs,sizeof(DAZZ_DB),1,ixfile)
     if (SELECT >= 0)
-      FWRITE(reads,sizeof(DAZZ_READ),nreads,ixfile)
+      FFWRITE(reads,sizeof(DAZZ_READ),nreads,ixfile)
   }
 
   FCLOSE(ixfile)

DBwipe.c

@@ -89,8 +89,8 @@ int main(int argc, char *argv[])
     if (index_name == NULL || index == NULL)
       exit (1);
 
-    FWRITE(&db,sizeof(DAZZ_DB),1,index)
-    FWRITE(db.reads,sizeof(DAZZ_READ),db.nreads,index)
+    FFWRITE(&db,sizeof(DAZZ_DB),1,index)
+    FFWRITE(db.reads,sizeof(DAZZ_READ),db.nreads,index)
 
     FCLOSE(index);
   }

Makefile

@@ -3,7 +3,7 @@ DEST_DIR = ~/bin
 CFLAGS = -O3 -Wall -Wextra -Wno-unused-result -fno-strict-aliasing
 
 ALL = fasta2DB DB2fasta quiva2DB DB2quiva DBsplit DBdust Catrack DBshow DBstats DBrm DBmv \
-      simulator fasta2DAM DAM2fasta DBdump rangen arrow2DB DB2arrow DBwipe DBtrim
+      simulator fasta2DAM DAM2fasta DBdump rangen arrow2DB DB2arrow DBwipe DBtrim DBa2b DBb2a
 
 all: $(ALL)
 
@@ -67,6 +67,11 @@ DAM2fasta: DAM2fasta.c DB.c DB.h QV.c QV.h
 DBwipe: DBwipe.c DB.c DB.h QV.c QV.h
 	gcc $(CFLAGS) -o DBwipe DBwipe.c DB.c QV.c -lm
 
+DBa2b: DBa2b.c DB.c DB.h QV.c QV.h
+	gcc $(CFLAGS) -o DBa2b DBa2b.c DB.c QV.c -lm
+
+DBb2a: DBb2a.c DB.c DB.h QV.c QV.h
+	gcc $(CFLAGS) -o DBb2a DBb2a.c DB.c QV.c -lm
 
 clean:
 	rm -f $(ALL)

README.md

@@ -2,6 +2,7 @@
 
 ## _Author:  Gene Myers_
 ## _First:   July 17, 2013_
+## _Current:   April 19, 2019_
 
 For typeset documentation, examples of use, and design philosophy please go to
 my [blog](https://dazzlerblog.wordpress.com/command-guides/dazz_db-command-guide).
@@ -157,7 +158,9 @@ in a given named input (i.e. all sources other than -i without a name) can only
 added consecutively to the DB (this is checked by the command). The .fasta headers must
 be in the "Pacbio" format (i.e. the output of the Pacbio tools or our dextract program)
 and the well, pulse interval, and read quality are extracted from the header and kept
-with each read record. If the files are being added to an existing database, and the
+with each read record.  The headers may now also be those Pacbio outputs for CCS data
+wherein the pulse range is replaced by the string "ccs" and in which case only the
+well number is recorded.  If the files are being added to an existing database, and the
 partition settings of the DB have already been set (see DBsplit below), then the
 partitioning of the database is updated to include the new data.  A file may contain
 the data from multiple SMRT cells provided the reads for each SMRT cell are consecutive
@@ -314,11 +317,12 @@ This permits job parallelism in block-sized chunks, and the resulting sequence o
 block tracks can then be merged into a track for the entire untrimmed DB with Catrack.
 
 ```
-12. Catrack [-vfd] <path:db|dam> <track:name>
+12. Catrack [-vfd] <path:db|dam> <track:name> ...
 ```
 
 Find all block tracks of the form .\<path\>.#.\<track\>... and concatenate them into a single
-track, .\<path\>.\<track\>..., for the given DB or DAM.   The block track files must all
+track, .\<path\>.\<track\>..., for the given DB or DAM.  Do so for each track name present on
+the command line.    The block track files must all
 encode the same kind of track data (this is checked), and the files must exist for
 block 1, 2, 3, ... up to the last block number.  If the -f option is set, then the
 concatenation takes place regardless of whether or not the single, combined track
@@ -365,7 +369,7 @@ fasta2DB, quiva2D, and arrow2DB, giving one a simple way to make a DB of a subse
 the reads for testing purposes.
 
 ```
-14. DBdump [-rhsaqip] [-uU] [-m<mask>]+
+14. DBdump [-rhsaqif] [-uU] [-m<mask>]+
                       <path:db|dam> [ <reads:FILE> | <reads:range> ... ]
 ```
 
@@ -390,7 +394,7 @@ the 4 SNR channel values on an N-line,
 
 * -i requests that the intrinsic quality values be output on an I-line.
 
-* -p requests the repeat profile be output (if available) on a P-line, on a P-line
+* -f requests the source file name is output just before the first read data in the file on a F-line.
 
 * -m\<track\> requests that mask \<track\> be output on a T-line.
 
@@ -404,9 +408,8 @@ separated by a single blank space.  Strings are output as first an integer givin
 length of the string, a blank space, and then the string terminated by a new-line.
 Intrinsic quality values are between 0 and 50, inclusive, and a vector of said are
 displayed as an alphabetic string where 'a' is 0, 'b' is '1', ... 'z' is 25, 'A' is
-26, 'B' is 27, ... and 'Y' is 50.  Repeat profiles are also displayed as string where
-'_' denotes 0 repetitions, and then 'a' through 'N' denote the values 1 through 40,
-respectively.   The set of all possible lines is as follows:
+26, 'B' is 27, ... and 'Y' is 50.
+The set of all possible lines is as follows:
 
 ```
     R #              - read number
@@ -418,28 +421,38 @@ respectively.   The set of all possible lines is as follows:
     S # string       - sequence string
     A # string       - arrow pulse-width string
     I # string       - intrinsic quality vector (as an ASCII string)
-    P # string       - repeat profile vector (as an ASCII string)
+    F # string       - name of source file of following data
     d # string       - Quiva deletion values (as an ASCII string)
     c # string       - Quiva deletion character string
     i # string       - Quiva insertion value string
     m # string       - Quiva merge value string
     s # string       - Quiva substitution value string
-    + X #            - Total amount of X (X = H or S or I or P or R or M or T#)
-    @ X #            - Maximum amount of X (X = H or S or I or P or T#)
+    + X #            - Total amount of X (X = H or S or I or F or R or M or T#)
+    @ X #            - Maximum amount of X (X = H or S or I or F or T#)
 ```
 
 1-code lines that begin with + or @ are always the first lines in the output.  They
 give size information about what is contained in the output.  That is '+ X #' gives
 the number of reads (X=R), the number of masks (X=M), or the total number of
 characters in all headers (X=H), sequences (X=S), intrinsic quality vectors (X=I),
-read profile vector (X=P), or track (X=T#).  And '@ X #' gives the maximum number of
-characters in any header (X=H), sequence (X=S), intrincic quality vector (X=I), read
-profile vector (X=P), or track (X=T#).  The size numbers for the Quiva strings and
+file names (X=F), or track (X=T#).  And '@ X #' gives the maximum number of
+characters in any header (X=H), sequence (X=S), intrincic quality vector (X=I),
+names (X=F), or track (X=T#).  The size numbers for the Quiva strings and
 Arrow pulse width strings are identical to that for the sequence as they are all of
 the same length for any given entry.
 
 ```
-15. DBstats [-nu] [-b<int(1000)] [-m<mask>]+ <path:db|dam>
+15a. DBa2b
+15b. DBb2a
+```
+
+Pipes (stdin to stdout) that convert an ASCII output produced by DBdump into a compressed
+binary representation (DBa2b) and vice verse (DBb2a).  The idea is to save disk space by
+keeping the dumps in a more compessed format.
+
+
+```
+16. DBstats [-nu] [-b<int(1000)] [-m<mask>]+ <path:db|dam>
 ```
 
 Show overview statistics for all the reads in the trimmed data base \<path\>.db or
@@ -451,7 +464,7 @@ intervals along the read can be specified with the -m option in which case a sum
 and a histogram of the interval lengths is displayed.
 
 ```
-16. DBrm [-v] <path:db|dam> ...
+17. DBrm [-v] <path:db|dam> ...
 ```
 
 Delete all the files for the given data bases.  Do not use rm to remove a database, as
@@ -460,14 +473,14 @@ files, and all of these are removed by DBrm.
 If the -v option is set then every file deleted is listed.
 
 ```
-17. DBmv [-v] <old:db|dam> <new:db|dam>
+18. DBmv [-v] <old:db|dam> <new:db|dam>
 ```
 
 Rename all the files for the data base old to use the new root.
 If the -v option is set then every file move is displayed.
 
 ```
-18. DBwipe <path:db|dam> ...
+19. DBwipe <path:db|dam>
 ```
 
 Delete any Arrow or Quiver data from the given databases.  This removes the .arw or
@@ -475,7 +488,7 @@ Delete any Arrow or Quiver data from the given databases.  This removes the .arw
 or Quiver.  Basically, converts an A-DB or Q-DB back to a simple S-DB.
 
 ```
-19.  simulator <genome:dam> [-CU] [-m<int(10000)>] [-s<int(2000)>] [-e<double(.15)]
+20.  simulator <genome:dam> [-CU] [-m<int(10000)>] [-s<int(2000)>] [-e<double(.15)]
                                   [-c<double(50.)>] [-f<double(.5)>] [-x<int(4000)>]
                                   [-w<int(80)>] [-r<int>] [-M<file>]
 ```
@@ -510,7 +523,7 @@ a read is say 's b e' then if b \< e the read is a perturbed copy of s[b,e] in t
 forward direction, and a perturbed copy s[e,b] in the reverse direction otherwise.
 
 ```
-20. rangen <genlen:double> [-U] [-b<double(.5)>] [-w<int(80)>] [-r<int>]
+21. rangen <genlen:double> [-U] [-b<double(.5)>] [-w<int(80)>] [-r<int>]
 ```
 
 Generate a random DNA sequence of length genlen*1Mbp that has an AT-bias of -b.

debian/changelog

+dazzdb (1.0+git20190616.034f1ab-1) unstable; urgency=medium
+
+  * Afif removed himself from Uploaders
+  * Add myself to Uploaders
+  * New upstream version
+  * debhelper-compat 12
+  * Standards-Version: 4.4.0
+
+ -- Andreas Tille <tille@debian.org>  Tue, 20 Aug 2019 12:37:09 +0200
+
 dazzdb (1.0+git20180908.0bd5e07-1) unstable; urgency=medium
 
   * Team upload.

debian/compat

-11

debian/control

 Source: dazzdb
 Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
+Uploaders: Andreas Tille <tille@debian.org>
 Section: science
 Priority: optional
-Build-Depends: debhelper (>= 11~),
+Build-Depends: debhelper-compat (= 12),
                zlib1g-dev
-Standards-Version: 4.2.1
+Standards-Version: 4.4.0
 Vcs-Browser: https://salsa.debian.org/med-team/dazzdb
 Vcs-Git: https://salsa.debian.org/med-team/dazzdb.git
 Homepage: https://github.com/thegenemyers/DAZZ_DB

debian/patches/append-cflags.patch

@@ -2,8 +2,8 @@ Description: Make upstream build system append to CFLAGS
 Author: Afif Elghraoui <afif@ghraoui.name>
 Forwarded: no
 Last-Update: 2015-09-13
---- dazzdb.orig/Makefile
-+++ dazzdb/Makefile
+--- a/Makefile
++++ b/Makefile
 @@ -1,6 +1,6 @@
  DEST_DIR = ~/bin
  
@@ -11,4 +11,4 @@ Last-Update: 2015-09-13
 +CFLAGS += -O3 -Wall -Wextra -Wno-unused-result -fno-strict-aliasing
  
  ALL = fasta2DB DB2fasta quiva2DB DB2quiva DBsplit DBdust Catrack DBshow DBstats DBrm DBmv \
-       simulator fasta2DAM DAM2fasta DBdump rangen arrow2DB DB2arrow DBwipe DBtrim
+       simulator fasta2DAM DAM2fasta DBdump rangen arrow2DB DB2arrow DBwipe DBtrim DBa2b DBb2a

debian/patches/compiler-flags.patch

@@ -2,8 +2,8 @@ Description: Honor LDFLAGS in upstream Makefile
 Author: Afif Elghraoui <afif@debian.org>
 Forwarded: https://github.com/thegenemyers/DAZZ_DB/pull/26
 Last-Update: 2017-01-18
---- dazzdb.orig/Makefile
-+++ dazzdb/Makefile
+--- a/Makefile
++++ b/Makefile
 @@ -1,6 +1,7 @@
  DEST_DIR = ~/bin
  
@@ -11,8 +11,8 @@ Last-Update: 2017-01-18
 +LDLIBS = -lm
  
  ALL = fasta2DB DB2fasta quiva2DB DB2quiva DBsplit DBdust Catrack DBshow DBstats DBrm DBmv \
-       simulator fasta2DAM DAM2fasta DBdump rangen arrow2DB DB2arrow DBwipe DBtrim
-@@ -8,64 +9,48 @@
+       simulator fasta2DAM DAM2fasta DBdump rangen arrow2DB DB2arrow DBwipe DBtrim DBa2b DBb2a
+@@ -8,64 +9,48 @@ ALL = fasta2DB DB2fasta quiva2DB DB2quiv
  all: $(ALL)
  
  fasta2DB: fasta2DB.c DB.c DB.h QV.c QV.h
@@ -79,5 +79,5 @@ Last-Update: 2017-01-18
  DBwipe: DBwipe.c DB.c DB.h QV.c QV.h
 -	gcc $(CFLAGS) -o DBwipe DBwipe.c DB.c QV.c -lm
  
- 
- clean:
+ DBa2b: DBa2b.c DB.c DB.h QV.c QV.h
+ 	gcc $(CFLAGS) -o DBa2b DBa2b.c DB.c QV.c -lm

debian/patches/destdir.patch

@@ -3,9 +3,9 @@ Description: Set destination directory in upstream Makefile
 Author: Afif Elghraoui <afif@ghraoui.name>
 Forwarded: no
 Last-Update: 2015-09-13
---- dazzdb.orig/Makefile
-+++ dazzdb/Makefile
-@@ -59,7 +59,8 @@
+--- a/Makefile
++++ b/Makefile
+@@ -64,7 +64,8 @@ clean:
  	rm -f dazz.db.tar.gz
  
  install: