.travis.yml

@@ -33,10 +33,10 @@ sudo: false
 # Copied from https://github.com/nim-lang/Nim/wiki/TravisCI
 #language: c
 env:
-  # Build and test against the master and devel branches of Nim
-  #- BRANCH=master
-  - BRANCH=devel
-  #- BRANCH=v0.17.2
+  # Build and test against the master and/or devel branches of Nim
+  - BRANCH=master
+  #- BRANCH=devel
+  #- BRANCH=v0.18.0
 compiler:
   # Build and test using both gcc and clang
   - gcc
@@ -76,8 +76,8 @@ before_script:
 #    - nim doc --docSeeSrcUrl:https://github.com/AUTHOR/MYPROJECT/blob/master --project MYFILE.nim
 cache:
   directories:
-    #- nim-master
-    - nim-devel
+    - nim-master
+    #- nim-devel
 branches:
   except:
     - gh-pages

DALIGNER/DB2Falcon.c

@@ -16,7 +16,7 @@
 static char *Usage = "[-U] [-w<int(80)>] <path:db>";
 
 int main(int argc, char *argv[])
-{ HITS_DB    _db, *db = &_db;
+{ DAZZ_DB    _db, *db = &_db;
   FILE       *dbfile;
   int         nfiles;
   int         UPPER, WIDTH;
@@ -83,7 +83,7 @@ int main(int argc, char *argv[])
 
   //  For each file do:
 
-  { HITS_READ  *reads;
+  { DAZZ_READ  *reads;
     char       *read;
     int         f, first;
     FILE *ofile;
@@ -107,7 +107,7 @@ int main(int argc, char *argv[])
 
         for (i = first; i < last && i <  db->nreads; i++)
           { int        j, len;
-            HITS_READ *r;
+            DAZZ_READ *r;
 
             r     = reads + i;
             len   = r->rlen;

DALIGNER/DBX.c

@@ -6,7 +6,7 @@
 #include <assert.h>
 
 // From Jason, with 1 change
-static char* Load_Read_Data(HITS_DB *db) {
+static char* Load_Read_Data(DAZZ_DB *db) {
   FILE  *bases  = (FILE*) db->bases;
   struct stat sbuf;
   char  *data;
@@ -22,7 +22,7 @@ static char* Load_Read_Data(HITS_DB *db) {
 }
 
 // Wrapper
-int Open_DBX(char *path, HITS_DBX *dbx, bool preload) {
+int Open_DBX(char *path, DAZZ_DBX *dbx, bool preload) {
   dbx->data = NULL;
   int rc = Open_DB(path, &dbx->db);
   switch (rc) {
@@ -44,10 +44,10 @@ int Open_DBX(char *path, HITS_DBX *dbx, bool preload) {
 }
 
 // From Jason
-static int Load_Read_From_RAM(HITS_DB *db, char *data, int i, char *read, int ascii) {
+static int Load_Read_From_RAM(DAZZ_DB *db, char *data, int i, char *read, int ascii) {
   int64      off;
   int        len, clen;
-  HITS_READ *r = db->reads;
+  DAZZ_READ *r = db->reads;
 
   if (i >= db->nreads) { EXIT(1); }
 
@@ -70,7 +70,7 @@ static int Load_Read_From_RAM(HITS_DB *db, char *data, int i, char *read, int as
 }
 
 // Wrapper
-int Load_ReadX(HITS_DBX *dbx, int i, char *read, int ascii) {
+int Load_ReadX(DAZZ_DBX *dbx, int i, char *read, int ascii) {
   if (dbx->data) {
     return Load_Read_From_RAM(&dbx->db, dbx->data, i, read, ascii);
   } else {
@@ -79,7 +79,7 @@ int Load_ReadX(HITS_DBX *dbx, int i, char *read, int ascii) {
 }
 
 // Wrapper
-void Close_DBX(HITS_DBX *dbx) {
+void Close_DBX(DAZZ_DBX *dbx) {
   Close_DB(&dbx->db);
   if (dbx->data) free(dbx->data);
 }

DALIGNER/DBX.h

 #ifndef DALIGNER_DBX_H
 #define DALIGNER_DBX_H
-/* Wrappers to extend HITS_DB.
+/* Wrappers to extend DAZZ_DB.
  *
  * Note that none of the extra fields are ever stored on-disk.
  */
@@ -8,18 +8,18 @@
 #include <stdbool.h>
 
 typedef struct {
-	HITS_DB db;
+	DAZZ_DB db;
 /*
  * When "data" is non-null, it stores the entire DB
  * in memory, so we can avoid random-access disk operations.
  * But if null, then wrappers simply delegate.
  */
 	char* data;
-} HITS_DBX;
+} DAZZ_DBX;
 
-int Open_DBX(char *path, HITS_DBX *dbx, bool preload);
-int  Load_ReadX(HITS_DBX *dbx, int i, char *read, int ascii);
-//void Trim_DB(HITS_DBX *dbx);
-void Close_DBX(HITS_DBX *dbx);
+int Open_DBX(char *path, DAZZ_DBX *dbx, bool preload);
+int  Load_ReadX(DAZZ_DBX *dbx, int i, char *read, int ascii);
+//void Trim_DB(DAZZ_DBX *dbx);
+void Close_DBX(DAZZ_DBX *dbx);
 
 #endif

DALIGNER/DISCLAIMER

+/*****************************************************************************\
+PacBio Disclaimer
+
+THIS WEBSITE AND CONTENT AND ALL SITE-RELATED SERVICES, INCLUDING ANY DATA, ARE
+PROVIDED "AS IS," WITH ALL FAULTS, WITH NO REPRESENTATIONS OR WARRANTIES OF ANY
+KIND, EITHER EXPRESS OR IMPLIED, INCLUDING, BUT NOT LIMITED TO, ANY WARRANTIES
+OF MERCHANTABILITY, SATISFACTORY QUALITY, NON-INFRINGEMENT OR FITNESS FOR A
+PARTICULAR PURPOSE. YOU ASSUME TOTAL RESPONSIBILITY AND RISK FOR YOUR USE OF
+THIS SITE, ALL SITE-RELATED SERVICES, AND ANY THIRD PARTY WEBSITES OR
+APPLICATIONS. NO ORAL OR WRITTEN INFORMATION OR ADVICE SHALL CREATE A WARRANTY
+OF ANY KIND. ANY REFERENCES TO SPECIFIC PRODUCTS OR SERVICES ON THE WEBSITES DO
+NOT CONSTITUTE OR IMPLY A RECOMMENDATION OR ENDORSEMENT BY PACIFIC BIOSCIENCES.
+\******************************************************************************/

DALIGNER/GNUmakefile

 THISDIR:=$(abspath $(dir $(realpath $(lastword ${MAKEFILE_LIST}))))
-LIBDIRS?=${THISDIR}/../DAZZ_DB
+#LIBDIRS?=${THISDIR}/../DAZZ_DB
 CFLAGS+= -O3 -Wall -Wextra -fno-strict-aliasing -Wno-unused-result
-CPPFLAGS+= -I${THISDIR}/../DAZZ_DB -I${PREFIX}/include
+#CPPFLAGS+= -I${THISDIR}/../DAZZ_DB -I${PREFIX}/include
 #CPPFLAGS+= -MMD -MP
-LDLIBS+= -ldazzdb -lm -lpthread
+LDLIBS+= -lm -lpthread
 LDFLAGS+= $(patsubst %,-L%,${LIBDIRS})
 MOST = daligner HPC.daligner LAsort LAmerge LAsplit LAcat LAshow LAdump LAcheck LAindex
 ALL:=${MOST} daligner_p LA4Falcon LA4Ice DB2Falcon
 vpath %.c ${THISDIR}
-vpath %.a ${THISDIR}/../DAZZ_DB
+#vpath %.a ${THISDIR}/../DAZZ_DB
 
 %: %.c
 
@@ -16,7 +16,9 @@ all: ${ALL}
 daligner: filter.o
 daligner_p: filter_p.o
 LA4Falcon: DBX.o
-${ALL}: align.o
+${ALL}: libdazzdb.a
+
+libdazzdb.a: libdazzdb.a(DB.o QV.o align.o)
 
 install:
 	rsync -av ${ALL} ${PREFIX}/bin
@@ -25,7 +27,7 @@ symlink:
 clean:
 	rm -f ${ALL}
 	rm -f ${DEPS}
-	rm -fr *.dSYM *.o *.d
+	rm -fr *.dSYM *.o *.d *.a
 
 .PHONY: clean all
 

DALIGNER/LA4Falcon.c

@@ -147,7 +147,7 @@ static bool add_overlap(const Alignment *aln, const Overlap *ovl, const int coun
     return added;
 }
 
-static void print_hits(const int hit_count, HITS_DBX *dbx2, char *bbuffer, char buffer[], int64 bsize, const int MAX_HIT_COUNT) {
+static void print_hits(const int hit_count, DAZZ_DBX *dbx2, char *bbuffer, char buffer[], int64 bsize, const int MAX_HIT_COUNT) {
     int tmp_idx;
     qsort(ovlgrps, (hit_count+1), sizeof(OverlapGroup), compare_ovlgrps);
     for (tmp_idx = 0; tmp_idx < (hit_count+1) && tmp_idx < MAX_HIT_COUNT; tmp_idx++) {
@@ -159,7 +159,7 @@ static void print_hits(const int hit_count, HITS_DBX *dbx2, char *bbuffer, char
         int64 const rlen = (int64)(grp->end.path.bepos) - (int64)(grp->beg.path.bbpos);
         if (rlen < bsize) {
             strncpy( buffer, bbuffer + grp->beg.path.bbpos, rlen );
-            buffer[rlen - 1] = '\0';
+            buffer[rlen] = '\0';
             printf("%08d %s\n", grp->end.bread, buffer);
         } else {
             fprintf(stderr, "[WARNING]Skipping super-long read %08d, len=%lld, buf=%lld\n", grp->end.bread, rlen, bsize);
@@ -182,10 +182,10 @@ static int ORDER(const void *l, const void *r)
 }
 
 int main(int argc, char *argv[])
-{ HITS_DBX   _dbx1, *dbx1 = &_dbx1;
-  HITS_DBX   _dbx2, *dbx2 = &_dbx2;
-  HITS_DB *db1 = &dbx1->db;
-  HITS_DB *db2 = &dbx2->db;
+{ DAZZ_DBX   _dbx1, *dbx1 = &_dbx1;
+  DAZZ_DBX   _dbx2, *dbx2 = &_dbx2;
+  DAZZ_DB *db1 = &dbx1->db;
+  DAZZ_DB *db2 = &dbx2->db;
   Overlap   _ovl, *ovl = &_ovl;
   Alignment _aln, *aln = &_aln;
 
@@ -457,9 +457,9 @@ int main(int argc, char *argv[])
       exit (1);
 
     if (fread(&novl,sizeof(int64),1,input) != 1)
-      SYSTEM_ERROR
+      SYSTEM_READ_ERROR
     if (fread(&tspace,sizeof(int),1,input) != 1)
-      SYSTEM_ERROR
+      SYSTEM_READ_ERROR
 
     if (tspace == 0) {
         printf("\nCRITICAL ERROR: tspace=0 in '%s'", root);

DALIGNER/LA4Ice.c

@@ -72,8 +72,8 @@ static int ORDER(const void *l, const void *r)
 }
 
 int main(int argc, char *argv[])
-{ HITS_DB   _db1, *db1 = &_db1; 
-  HITS_DB   _db2, *db2 = &_db2; 
+{ DAZZ_DB   _db1, *db1 = &_db1; 
+  DAZZ_DB   _db2, *db2 = &_db2; 
   Overlap   _ovl, *ovl = &_ovl;
   Alignment _aln, *aln = &_aln;
 
@@ -259,9 +259,9 @@ int main(int argc, char *argv[])
       exit (1);
 
     if (fread(&novl,sizeof(int64),1,input) != 1)
-      SYSTEM_ERROR
+      SYSTEM_READ_ERROR
     if (fread(&tspace,sizeof(int),1,input) != 1)
-      SYSTEM_ERROR
+      SYSTEM_READ_ERROR
 
     if (tspace <= TRACE_XOVR)
       { small  = 1;

DALIGNER/LAcat.c

@@ -90,13 +90,13 @@ int main(int argc, char *argv[])
         if ((input = fopen(name,"r")) == NULL) break;
 
         if (fread(&povl,sizeof(int64),1,input) != 1)
-          SYSTEM_ERROR
+          SYSTEM_READ_ERROR
         novl += povl;
         if (fread(&mspace,sizeof(int),1,input) != 1)
-          SYSTEM_ERROR
+          SYSTEM_READ_ERROR
         if (i == 0)
           { tspace = mspace;
-            if (tspace <= TRACE_XOVR)
+            if (tspace <= TRACE_XOVR && tspace != 0)
               tbytes = sizeof(uint8);
             else
               tbytes = sizeof(uint16);
@@ -108,8 +108,10 @@ int main(int argc, char *argv[])
 
         fclose(input);
       }
-    fwrite(&novl,sizeof(int64),1,stdout);
-    fwrite(&tspace,sizeof(int),1,stdout);
+    if (fwrite(&novl,sizeof(int64),1,stdout) != 1)
+      SYSTEM_READ_ERROR
+    if (fwrite(&tspace,sizeof(int),1,stdout) != 1)
+      SYSTEM_READ_ERROR
   }
 
   { int      i, j;
@@ -127,9 +129,9 @@ int main(int argc, char *argv[])
         if ((input = fopen(name,"r")) == NULL) break;
 
         if (fread(&povl,sizeof(int64),1,input) != 1)
-          SYSTEM_ERROR
+          SYSTEM_READ_ERROR
         if (fread(&mspace,sizeof(int),1,input) != 1)
-          SYSTEM_ERROR
+          SYSTEM_READ_ERROR
 
         if (VERBOSE)
           fprintf(stderr,"  Concatenating %s: %lld la\'s\n",Numbered_Suffix(root,i+1,root2),povl);
@@ -141,7 +143,7 @@ int main(int argc, char *argv[])
           { if (iptr + ovlsize > itop)
               { int64 remains = itop-iptr;
                 if (remains > 0)
-                  memcpy(iblock,iptr,remains);
+                  memmove(iblock,iptr,remains);
                 iptr  = iblock;
                 itop  = iblock + remains;
                 itop += fread(itop,1,bsize-remains,input);
@@ -151,24 +153,25 @@ int main(int argc, char *argv[])
             tsize = w->path.tlen*tbytes;
 
             if (optr + ovlsize + tsize > otop)
-              { fwrite(oblock,1,optr-oblock,stdout);
+              { if (fwrite(oblock,1,optr-oblock,stdout) != (size_t) (optr-oblock))
+                  SYSTEM_READ_ERROR
                 optr = oblock;
               }
 
-            memcpy(optr,iptr,ovlsize);
+            memmove(optr,iptr,ovlsize);
             optr += ovlsize;
             iptr += ovlsize;
 
             if (iptr + tsize > itop)
               { int64 remains = itop-iptr;
                 if (remains > 0)
-                  memcpy(iblock,iptr,remains);
+                  memmove(iblock,iptr,remains);
                 iptr  = iblock;
                 itop  = iblock + remains;
                 itop += fread(itop,1,bsize-remains,input);
               }
             
-            memcpy(optr,iptr,tsize);
+            memmove(optr,iptr,tsize);
             optr += tsize;
             iptr += tsize;
           }
@@ -177,7 +180,9 @@ int main(int argc, char *argv[])
       }
 
     if (optr > oblock)
-      fwrite(oblock,1,optr-oblock,stdout);
+      { if (fwrite(oblock,1,optr-oblock,stdout) != (size_t) (optr-oblock))
+          SYSTEM_READ_ERROR
+      }
   }
 
   if (VERBOSE)

DALIGNER/LAcheck.c

@@ -23,8 +23,8 @@ static char *Usage = "[-vS] <src1:db|dam> [ <src2:db|dam> ] <align:las> ...";
 #define MEMORY   1000   //  How many megabytes for output buffer
 
 int main(int argc, char *argv[])
-{ HITS_DB   _db1,  *db1  = &_db1;
-  HITS_DB   _db2,  *db2  = &_db2;
+{ DAZZ_DB   _db1,  *db1  = &_db1;
+  DAZZ_DB   _db2,  *db2  = &_db2;
   int        VERBOSE;
   int        SORTED;
   int        ISTWO;
@@ -103,9 +103,9 @@ int main(int argc, char *argv[])
   { char      *iblock;
     int64      bsize, ovlsize, ptrsize;
     int        i, j;
-    HITS_READ *reads1  = db1->reads;
+    DAZZ_READ *reads1  = db1->reads;
     int        nreads1 = db1->nreads;
-    HITS_READ *reads2  = db2->reads;
+    DAZZ_READ *reads2  = db2->reads;
     int        nreads2 = db2->nreads;
 
     //  Setup IO buffers
@@ -138,9 +138,9 @@ int main(int argc, char *argv[])
           goto error;
 
         if (fread(&novl,sizeof(int64),1,input) != 1)
-          SYSTEM_ERROR
+          SYSTEM_READ_ERROR
         if (fread(&tspace,sizeof(int),1,input) != 1)
-          SYSTEM_ERROR
+          SYSTEM_READ_ERROR
         if (novl < 0)
           { if (VERBOSE)
               fprintf(stderr,"  %s: Number of alignments < 0\n",root);
@@ -152,7 +152,7 @@ int main(int argc, char *argv[])
             goto error;
           }
 
-        if (tspace <= TRACE_XOVR)
+        if (tspace <= TRACE_XOVR && tspace != 0)
           tbytes = sizeof(uint8);
         else
           tbytes = sizeof(uint16);
@@ -179,7 +179,7 @@ int main(int argc, char *argv[])
             if (iptr + ovlsize > itop)
               { int64 remains = itop-iptr;
                 if (remains > 0)
-                  memcpy(iblock,iptr,remains);
+                  memmove(iblock,iptr,remains);
                 iptr  = iblock;
                 itop  = iblock + remains;
                 itop += fread(itop,1,bsize-remains,input);
@@ -197,7 +197,7 @@ int main(int argc, char *argv[])
             if (iptr + tsize > itop)
               { int64 remains = itop-iptr;
                 if (remains > 0)
-                  memcpy(iblock,iptr,remains);
+                  memmove(iblock,iptr,remains);
                 iptr  = iblock;
                 itop  = iblock + remains;
                 itop += fread(itop,1,bsize-remains,input);

DALIGNER/LAdump.c

@@ -22,7 +22,7 @@
 #include "align.h"
 
 static char *Usage =
-    "[-cdt] [-o] <src1:db|dam> [ <src2:db|dam> ] <align:las> [ <reads:FILE> | <reads:range> ... ]";
+    "[-cdtlo] <src1:db|dam> [<src2:db|dam>] <align:las> [<reads:FILE> | <reads:range> ...]";
 
 #define LAST_READ_SYMBOL  '$'
 
@@ -33,18 +33,19 @@ static int ORDER(const void *l, const void *r)
 }
 
 int main(int argc, char *argv[])
-{ HITS_DB   _db1, *db1 = &_db1; 
-  HITS_DB   _db2, *db2 = &_db2; 
+{ DAZZ_DB   _db1, *db1 = &_db1; 
+  DAZZ_DB   _db2, *db2 = &_db2; 
   Overlap   _ovl, *ovl = &_ovl;
 
   FILE   *input;
   int64   novl;
   int     tspace, tbytes, small;
+  int     tmax;
   int     reps, *pts;
   int     input_pts;
 
   int     OVERLAP;
-  int     DOCOORDS, DODIFFS, DOTRACE;
+  int     DOCOORDS, DODIFFS, DOTRACE, DOLENS;
   int     ISTWO;
 
   //  Process options
@@ -59,7 +60,7 @@ int main(int argc, char *argv[])
       if (argv[i][0] == '-')
         switch (argv[i][1])
         { default:
-            ARG_FLAGS("ocdtUF")
+            ARG_FLAGS("ocdtl")
             break;
         }
       else
@@ -70,12 +71,33 @@ int main(int argc, char *argv[])
     DOCOORDS  = flags['c'];
     DODIFFS   = flags['d'];
     DOTRACE   = flags['t'];
+    DOLENS    = flags['l'];
 
     if (DOTRACE)
       DOCOORDS = 1;
 
     if (argc <= 2)
       { fprintf(stderr,"Usage: %s %s\n",Prog_Name,Usage);
+        fprintf(stderr,"\n");
+        fprintf(stderr,"      P #a #b #o #c     -");
+        fprintf(stderr," (#a,#b^#o) have an LA between them where #o is 'n' or 'c' and\n");
+        fprintf(stderr,"                         ");
+        fprintf(stderr,"   #c is '>' (start of best chain), '+' (start of alternate chain),\n");
+        fprintf(stderr,"                         ");
+        fprintf(stderr,"   '-' (continuation of chain), or '.' (no chains in file).\n");
+        fprintf(stderr,"\n");
+        fprintf(stderr,"      -c: C #ab #ae #bb #be - #a[#ab,#ae] aligns with #b^#o[#bb,#be]\n");
+        fprintf(stderr,"      -d: D #               - there are # differences in the LA\n");
+        fprintf(stderr,"      -t: T #n              -");
+        fprintf(stderr," there are #n trace point intervals for the LA\n");
+        fprintf(stderr,"           (#d #y )^#n      -");
+        fprintf(stderr," there are #d difference aligning the #y bp's of B with the\n");
+        fprintf(stderr,"                                 next fixed-size interval of A\n");
+        fprintf(stderr,"      -l: L #la #lb         -");
+        fprintf(stderr," #la is the length of the a-read and #lb that of the b-read\n");
+        fprintf(stderr,"\n");
+        fprintf(stderr,"      -o: Output proper overlaps only\n");
+
         exit (1);
       }
   }
@@ -258,11 +280,11 @@ int main(int argc, char *argv[])
       exit (1);
 
     if (fread(&novl,sizeof(int64),1,input) != 1)
-      SYSTEM_ERROR
+      SYSTEM_READ_ERROR
     if (fread(&tspace,sizeof(int),1,input) != 1)
-      SYSTEM_ERROR
+      SYSTEM_READ_ERROR
 
-    if (tspace <= TRACE_XOVR)
+    if (tspace <= TRACE_XOVR && tspace != 0)
       { small  = 1;
         tbytes = sizeof(uint8);
       }
@@ -279,7 +301,7 @@ int main(int argc, char *argv[])
 
   { int   j, al, tlen;
     int   in, npt, idx, ar;
-    int64 novls, odeg, omax, sdeg, smax, ttot, tmax;
+    int64 novls, odeg, omax, sdeg, smax, ttot;
 
     in  = 0;
     npt = pts[0];
@@ -359,32 +381,31 @@ int main(int argc, char *argv[])
 
     printf("+ P %lld\n",novls);
     printf("%% P %lld\n",omax);
-    printf("+ T %lld\n",ttot);
+    if (DOTRACE)
+      { printf("+ T %lld\n",ttot);
         printf("%% T %lld\n",smax);
-    printf("@ T %lld\n",tmax);
+        printf("@ T %d\n",tmax);
+      }
   }
 
   //  Read the file and display selected records
   
-  { int        j;
+  { int        j, k;
     uint16    *trace;
-    int        tmax;
     int        in, npt, idx, ar;
-    int64      verse;
+    DAZZ_READ *read1, *read2;
 
     rewind(input);
-    fread(&verse,sizeof(int64),1,input);
+    fread(&novl,sizeof(int64),1,input);
     fread(&tspace,sizeof(int),1,input);
-    if (verse < 0)
-      { for (j = 0; j < 5; j++)
-          fread(&verse,sizeof(int64),1,input);
-      }
 
-    tmax  = 1000;
     trace = (uint16 *) Malloc(sizeof(uint16)*tmax,"Allocating trace vector");
     if (trace == NULL)
       exit (1);
 
+    read1 = db1->reads;
+    read2 = db2->reads;
+
     in  = 0;
     npt = pts[0];
     idx = 1;
@@ -396,12 +417,6 @@ int main(int argc, char *argv[])
        //  Read it in
 
       { Read_Overlap(input,ovl);
-        if (ovl->path.tlen > tmax)
-          { tmax = ((int) 1.2*ovl->path.tlen) + 100;
-            trace = (uint16 *) Realloc(trace,sizeof(uint16)*tmax,"Allocating trace vector");
-            if (trace == NULL)
-              exit (1);
-          }
         ovl->path.trace = (void *) trace;
         Read_Trace(input,ovl,tbytes);
 
@@ -458,6 +473,9 @@ int main(int argc, char *argv[])
           printf(" .");
         printf("\n");
 
+        if (DOLENS)
+          printf("L %d %d\n",read1[ovl->aread].rlen,read2[ovl->bread].rlen);
+
         if (DOCOORDS)
           printf("C %d %d %d %d\n",ovl->path.abpos,ovl->path.aepos,ovl->path.bbpos,ovl->path.bepos);
 
@@ -471,8 +489,8 @@ int main(int argc, char *argv[])
             if (small)
               Decompress_TraceTo16(ovl);
             printf("T %d\n",tlen>>1);
-            for (j = 0; j < tlen; j += 2)
-              printf(" %3d %3d\n",trace[j],trace[j+1]);
+            for (k = 0; k < tlen; k += 2)
+              printf(" %3d %3d\n",trace[k],trace[k+1]);
           }
       }
 

DALIGNER/LAindex.c

@@ -80,10 +80,10 @@ int main(int argc, char *argv[])
         exit (1);
     
       if (fread(&novl,sizeof(int64),1,input) != 1)
-        SYSTEM_ERROR
+        SYSTEM_READ_ERROR
       if (fread(&tspace,sizeof(int),1,input) != 1)
-        SYSTEM_ERROR
-      if (tspace <= TRACE_XOVR)
+        SYSTEM_READ_ERROR
+      if (tspace <= TRACE_XOVR && tspace != 0)
         tbytes = sizeof(uint8);
       else
         tbytes = sizeof(uint16);
@@ -126,7 +126,7 @@ int main(int argc, char *argv[])
           { if (iptr + ovlsize > itop)
               { int64 remains = itop-iptr;
                 if (remains > 0)
-                  memcpy(iblock,iptr,remains);
+                  memmove(iblock,iptr,remains);
                 iptr  = iblock;
                 itop  = iblock + remains;
                 itop += fread(itop,1,bsize-remains,input);
@@ -161,7 +161,7 @@ int main(int argc, char *argv[])
             if (iptr + tsize > itop)
               { int64 remains = itop-iptr;
                 if (remains > 0)
-                  memcpy(iblock,iptr,remains);
+                  memmove(iblock,iptr,remains);
                 iptr  = iblock;
                 itop  = iblock + remains;
                 itop += fread(itop,1,bsize-remains,input);

DALIGNER/LAmerge.c

@@ -48,24 +48,6 @@ static char *Usage = "[-va] <merge:las> <parts:las> ...";
   else						\
     bigger = 0;
 
-static void Fwrite(const void *ptr, size_t size, size_t nmemb, FILE *stream) {
-  size_t rc = fwrite(ptr, size, nmemb, stream);
-  if (rc != nmemb) {
-    EPRINTF(EPLACE,"  Error writing %zu elements (of size %zu)\n", nmemb, size);
-    exit(1);
-  }
-}
-
-static void Fclose(FILE *stream) {
-  // An error in fclose() could be caused by an earlier failure in fwrite().
-  // 'man fclose' for details.
-  int rc = fclose(stream);
-  if (rc != 0) {
-    EPRINTF(EPLACE,"  Error closing stream.\n");
-    exit(1);
-  }
-}
-
 static void reheap(int s, Overlap **heap, int hsize)
 { int      c, l, r;
   int      bigger;
@@ -266,18 +248,17 @@ int main(int argc, char *argv[])
       input = Fopen(Catenate(pwd,"/",root,".las"),"r");
       if (input == NULL)
         exit (1);
+      free(pwd);
+      free(root);
 
       if (fread(&novl,sizeof(int64),1,input) != 1)
-        SYSTEM_ERROR
+        SYSTEM_READ_ERROR
       totl += novl;
-      if (VERBOSE) fprintf(stdout, "In file %s, there are %lld records\n", Catenate(pwd,"/",root,".las"), novl);
-      free(pwd);
-      free(root);
       if (fread(&mspace,sizeof(int),1,input) != 1)
-        SYSTEM_ERROR
+        SYSTEM_READ_ERROR
       if (i == 0)
         { tspace = mspace;
-          if (tspace <= TRACE_XOVR)
+          if (tspace <= TRACE_XOVR && tspace != 0)
             tbytes = sizeof(uint8);
           else
             tbytes = sizeof(uint16);
@@ -306,8 +287,10 @@ int main(int argc, char *argv[])
     free(pwd);
     free(root);
 
-    Fwrite(&totl,sizeof(int64),1,output);
-    Fwrite(&tspace,sizeof(int),1,output);
+    if (fwrite(&totl,sizeof(int64),1,output) != 1)
+      SYSTEM_READ_ERROR
+    if (fwrite(&tspace,sizeof(int),1,output) != 1)
+      SYSTEM_READ_ERROR
 
     oblock = block+fway*bsize;
     optr   = oblock;
@@ -369,13 +352,14 @@ int main(int argc, char *argv[])
           if (src->ptr + span > src->top)
             ovl_reload(src,bsize);
           if (optr + span > otop)
-            { Fwrite(oblock,1,optr-oblock,output);
+            { if (fwrite(oblock,1,optr-oblock,output) != (size_t) (optr-oblock))
+                SYSTEM_READ_ERROR
               optr = oblock;
             }
 
-          memcpy(optr,((char *) ov) + psize,osize);
+          memmove(optr,((char *) ov) + psize,osize);
           optr += osize;
-          memcpy(optr,src->ptr,tsize);
+          memmove(optr,src->ptr,tsize);
           optr += tsize;
 
           src->ptr += tsize;
@@ -393,8 +377,10 @@ int main(int argc, char *argv[])
   //  Flush output buffer and wind up
 
   if (optr > oblock)
-    Fwrite(oblock,1,optr-oblock,output);
-  Fclose(output);
+    { if (fwrite(oblock,1,optr-oblock,output) != (size_t) (optr-oblock))
+        SYSTEM_READ_ERROR
+    }
+  fclose(output);
 
   for (i = 0; i < fway; i++)
     fclose(in[i].stream);

DALIGNER/LAshow.c

@@ -35,8 +35,8 @@ static int ORDER(const void *l, const void *r)
 }
 
 int main(int argc, char *argv[])
-{ HITS_DB   _db1, *db1 = &_db1; 
-  HITS_DB   _db2, *db2 = &_db2; 
+{ DAZZ_DB   _db1, *db1 = &_db1; 
+  DAZZ_DB   _db2, *db2 = &_db2; 
   Overlap   _ovl, *ovl = &_ovl;
   Alignment _aln, *aln = &_aln;
 
@@ -284,15 +284,15 @@ int main(int argc, char *argv[])
       exit (1);
 
     if (fread(&novl,sizeof(int64),1,input) != 1)
-      SYSTEM_ERROR
+      SYSTEM_READ_ERROR
     if (fread(&tspace,sizeof(int),1,input) != 1)
-      SYSTEM_ERROR
-    if (tspace <= 0)
-      { fprintf(stderr,"%s: Garbage .las file, trace spacing <= 0 !\n",Prog_Name);
+      SYSTEM_READ_ERROR
+    if (tspace < 0)
+      { fprintf(stderr,"%s: Garbage .las file, trace spacing < 0 !\n",Prog_Name);
         exit (1);
       }
 
-    if (tspace <= TRACE_XOVR)
+    if (tspace <= TRACE_XOVR && tspace != 0)
       { small  = 1;
         tbytes = sizeof(uint8);
       }
@@ -353,12 +353,18 @@ int main(int argc, char *argv[])
     if (db1->maxlen < db2->maxlen)
       { mn_wide = ai_wide;
         mx_wide = bi_wide;
+        if (tspace > 0)
           tp_wide = Number_Digits((int64) db1->maxlen/tspace+2);
+        else
+          tp_wide = 0;
       }
     else
       { mn_wide = bi_wide;
         mx_wide = ai_wide;
+        if (tspace > 0)
           tp_wide = Number_Digits((int64) db2->maxlen/tspace+2);
+        else
+          tp_wide = 0;
       }
     ar_wide += (ar_wide-1)/3;
     br_wide += (br_wide-1)/3;
@@ -393,6 +399,15 @@ int main(int argc, char *argv[])
         ovl->path.trace = (void *) trace;
         Read_Trace(input,ovl,tbytes);
 
+        if (ovl->aread >= db1->nreads)
+          { fprintf(stderr,"%s: A-read is out-of-range of DB %s\n",Prog_Name,argv[1]);
+            exit (1);
+          }
+        if (ovl->bread >= db2->nreads)
+          { fprintf(stderr,"%s: B-read is out-of-range of DB %s\n",Prog_Name,argv[1+ISTWO]);
+            exit (1);
+          }
+
         //  Determine if it should be displayed
 
         ar = ovl->aread+1;
@@ -514,15 +529,27 @@ int main(int argc, char *argv[])
         else
           printf("]");
 
+        if (!CARTOON)
+          printf("  ~  %5.2f%% ",(200.*ovl->path.diffs) /
+                 ((ovl->path.aepos - ovl->path.abpos) + (ovl->path.bepos - ovl->path.bbpos)) );
+        printf("  (");
+        if (FLIP)
+          { Print_Number(aln->alen,ai_wide,stdout);
+            printf(" x ");
+            Print_Number(aln->blen,bi_wide,stdout);
+          }
+        else
+          { Print_Number(aln->blen,bi_wide,stdout);
+            printf(" x ");
+            Print_Number(aln->alen,ai_wide,stdout);
+          }
+        printf(" bps,");
         if (CARTOON)
-          { printf("  (");
-            Print_Number(tps,tp_wide,stdout);
+          { Print_Number(tps,tp_wide,stdout);
             printf(" trace pts)\n\n");
           }
         else
-          { printf("  ~  %4.1f%%   (",(200.*ovl->path.diffs) /
-                    ((ovl->path.aepos - ovl->path.abpos) + (ovl->path.bepos - ovl->path.bbpos)) );
-            Print_Number((int64) ovl->path.diffs,mn_wide,stdout);
+          { Print_Number((int64) ovl->path.diffs,mn_wide,stdout);
             printf(" diffs, ");
             Print_Number(tps,tp_wide,stdout);
             printf(" trace pts)\n");
@@ -581,6 +608,9 @@ int main(int argc, char *argv[])
                 else
                   aln->bseq = bseq - bmin;
 
+                if (tspace == 0)
+                  Compute_Trace_IRR(aln,work,GREEDIEST);
+                else
                   Compute_Trace_PTS(aln,work,tspace,GREEDIEST);
 
                 if (FLIP)

DALIGNER/LAsort.c

@@ -25,24 +25,6 @@ static char *Usage = "[-va] <align:las> ...";
 
 static char *IBLOCK;
 
-static void Fwrite(const void *ptr, size_t size, size_t nmemb, FILE *stream) {
-  size_t rc = fwrite(ptr, size, nmemb, stream);
-  if (rc != nmemb) {
-    EPRINTF(EPLACE,"  Error writing %zu elements (of size %zu)\n", nmemb, size);
-    exit(1);
-  }
-}
-
-static void Fclose(FILE *stream) {
-  // An error in fclose() could be caused by an earlier failure in fwrite().
-  // 'man fclose' for details.
-  int rc = fclose(stream);
-  if (rc != 0) {
-    EPRINTF(EPLACE,"  Error closing stream.\n");
-    exit(1);
-  }
-}
-
 static int SORT_OVL(const void *x, const void *y)
 { int64 l = *((int64 *) x);
   int64 r = *((int64 *) y);
@@ -67,7 +49,7 @@ static int SORT_OVL(const void *x, const void *y)
     return (bl-br);
 
   cl = COMP(ol->flags);
-  cr = COMP(ol->flags);
+  cr = COMP(or->flags);
   if (cl != cr)
     return (cl-cr);
 
@@ -178,11 +160,11 @@ int main(int argc, char *argv[])
         size = info.st_size;
 
         if (fread(&novl,sizeof(int64),1,input) != 1)
-          SYSTEM_ERROR
+          SYSTEM_READ_ERROR
         if (fread(&tspace,sizeof(int),1,input) != 1)
-          SYSTEM_ERROR
+          SYSTEM_READ_ERROR
 
-        if (tspace <= TRACE_XOVR)
+        if (tspace <= TRACE_XOVR && tspace != 0)
           tbytes = sizeof(uint8);
         else
           tbytes = sizeof(uint16);
@@ -200,8 +182,10 @@ int main(int argc, char *argv[])
         if (foutput == NULL)
           exit (1);
 
-        Fwrite(&novl,sizeof(int64),1,foutput);
-        Fwrite(&tspace,sizeof(int),1,foutput);
+        if (fwrite(&novl,sizeof(int64),1,foutput) != 1)
+          SYSTEM_READ_ERROR
+        if (fwrite(&tspace,sizeof(int),1,foutput) != 1)
+          SYSTEM_READ_ERROR
 
         free(pwd);
         free(root);
@@ -219,7 +203,7 @@ int main(int argc, char *argv[])
         size -= (sizeof(int64) + sizeof(int));
         if (size > 0)
           { if (fread(iblock,size,1,input) != 1)
-              SYSTEM_ERROR
+              SYSTEM_READ_ERROR
           }
         fclose(input);
         iend = iblock + (size - ptrsize);
@@ -276,23 +260,26 @@ int main(int argc, char *argv[])
               { tsize = w->path.tlen*tbytes;
                 span  = ovlsize + tsize;
                 if (fptr + span > ftop)
-                  { Fwrite(fblock,1,fptr-fblock,foutput);
+                  { if (fwrite(fblock,1,fptr-fblock,foutput) != (size_t) (fptr-fblock))
+                      SYSTEM_READ_ERROR
                     fptr = fblock;
                   }
-                memcpy(fptr,((char *) w)+ptrsize,ovlsize);
+                memmove(fptr,((char *) w)+ptrsize,ovlsize);
                 fptr += ovlsize;
-                memcpy(fptr,(char *) (w+1),tsize);
+                memmove(fptr,(char *) (w+1),tsize);
                 fptr += tsize;
                 w = (Overlap *) (wo += span);
               }
             while (wo < iend && CHAIN_NEXT(w->flags));
           }
         if (fptr > fblock)
-          Fwrite(fblock,1,fptr-fblock,foutput);
+          { if (fwrite(fblock,1,fptr-fblock,foutput) != (size_t) (fptr-fblock))
+              SYSTEM_READ_ERROR
+          }
       }
 
       free(perm);
-      Fclose(foutput);
+      fclose(foutput);
     }
 
   if (iblock != NULL)

DALIGNER/LAsplit.c

@@ -81,19 +81,19 @@ int main(int argc, char *argv[])
         free(root);
 
         if (fscanf(dbvis,DB_NFILE,&nfiles) != 1)
-          SYSTEM_ERROR
+          SYSTEM_READ_ERROR
         while (nfiles-- > 0)
           if (fgets(buffer,2*MAX_NAME+100,dbvis) == NULL)
-            SYSTEM_ERROR
+            SYSTEM_READ_ERROR
         parts = 0;
         if (fscanf(dbvis,DB_NBLOCK,&parts) != 1)
           { fprintf(stderr,"%s: DB %s has not been partitioned\n",Prog_Name,argv[2]);
             exit (1);
           }
         if (fscanf(dbvis,DB_PARAMS,&size,&cutoff,&all) != 3)
-          SYSTEM_ERROR
+          SYSTEM_READ_ERROR
         if (fscanf(dbvis,DB_BDATA,&olast,&blast) != 2)
-          SYSTEM_ERROR
+          SYSTEM_READ_ERROR
       }
     else
       { dbvis = NULL;
@@ -128,10 +128,10 @@ int main(int argc, char *argv[])
   *root2++ = '\0';
 
   if (fread(&novl,sizeof(int64),1,stdin) != 1)
-    SYSTEM_ERROR
+    SYSTEM_READ_ERROR
   if (fread(&tspace,sizeof(int),1,stdin) != 1)
-    SYSTEM_ERROR
-  if (tspace <= TRACE_XOVR)
+    SYSTEM_READ_ERROR
+  if (tspace <= TRACE_XOVR && tspace != 0)
     tbytes = sizeof(uint8);
   else
     tbytes = sizeof(uint16);
@@ -139,9 +139,9 @@ int main(int argc, char *argv[])
   if (VERBOSE)
     fprintf(stderr,"  Distributing %lld la\'s\n",novl);
 
-  { int      i, j;
+  { int      i;
     Overlap *w;
-    int      low, hgh, last;
+    int64    j, low, hgh, last;
     int64    tsize, povl;
     char    *iptr, *itop;
     char    *optr, *otop;
@@ -158,7 +158,7 @@ int main(int argc, char *argv[])
         low = hgh;
         if (dbvis != NULL)
           { if (fscanf(dbvis,DB_BDATA,&olast,&blast) != 2)
-              SYSTEM_ERROR
+              SYSTEM_READ_ERROR
             last = blast-1;
             hgh  = 0;
           }
@@ -178,7 +178,7 @@ int main(int argc, char *argv[])
           { if (iptr + ovlsize > itop)
               { int64 remains = itop-iptr;
                 if (remains > 0)
-                  memcpy(iblock,iptr,remains);
+                  memmove(iblock,iptr,remains);
                 iptr  = iblock;
                 itop  = iblock + remains;
                 itop += fread(itop,1,bsize-remains,stdin);
@@ -201,19 +201,19 @@ int main(int argc, char *argv[])
                 optr = oblock;
               }
             
-            memcpy(optr,iptr,ovlsize);
+            memmove(optr,iptr,ovlsize);
             optr += ovlsize;
             iptr += ovlsize;
 
             if (iptr + tsize > itop)
               { int64 remains = itop-iptr;
                 if (remains > 0)
-                  memcpy(iblock,iptr,remains);
+                  memmove(iblock,iptr,remains);
                 iptr  = iblock;
                 itop  = iblock + remains;
                 itop += fread(itop,1,bsize-remains,stdin);
               }
-	    memcpy(optr,iptr,tsize);
+	    memmove(optr,iptr,tsize);
             optr += tsize;
             iptr += tsize;
           }

DALIGNER/Makefile

@@ -50,4 +50,4 @@ install:
 
 package:
 	make clean
-	tar -zcf daligner.tar.gz README Makefile *.h *.c
+	tar -zcf daligner.tar.gz README.md Makefile *.h *.c