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LAcheck.c
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LAcheck.c
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/*******************************************************************************************
*
* Check the structural integrity of .las files
*
* Author: Gene Myers
* Date : July 2014
*
*******************************************************************************************/
#include <stdio.h>
#include <stdlib.h>
#include <string.h>
#include <ctype.h>
#include <unistd.h>
#include <sys/types.h>
#include <sys/stat.h>
#include "DB.h"
#include "align.h"
static char *Usage = "[-vaS] <src1:db|dam> [ <src2:db|dam> ] <align:las> ...";
#define MEMORY 1000 // How many megabytes for output buffer
int main(int argc, char *argv[])
{ DAZZ_DB _db1, *db1 = &_db1;
DAZZ_DB _db2, *db2 = &_db2;
int VERBOSE;
int MAP_ORDER;
int SORTED;
int ISTWO;
int status;
// Process options
{ int i, j, k;
int flags[128];
ARG_INIT("LAcheck")
j = 1;
for (i = 1; i < argc; i++)
if (argv[i][0] == '-')
switch (argv[i][1])
{ default:
ARG_FLAGS("vaS")
break;
}
else
argv[j++] = argv[i];
argc = j;
VERBOSE = flags['v'];
MAP_ORDER = flags['a'];
SORTED = flags['S'];
if (argc <= 2)
{ fprintf(stderr,"Usage: %s %s\n",Prog_Name,Usage);
fprintf(stderr,"\n");
fprintf(stderr," -v: Verbose mode, output error messages.\n");
fprintf(stderr," -S: Check that .las is in sorted order.\n");
fprintf(stderr," -a: If -S, then check sorted by A-read, A-position pairs\n");
fprintf(stderr," off => check sorted by A,B-read pairs (LA-piles)\n");
exit (1);
}
}
// Open trimmed DB
{ Block_Looper *parse;
int status;
ISTWO = 0;
status = Open_DB(argv[1],db1);
if (status < 0)
exit (1);
if (db1->part > 0)
{ fprintf(stderr,"%s: Cannot be called on a block: %s\n",Prog_Name,argv[1]);
exit (1);
}
if (argc <= 3)
db2 = db1;
else
{ parse = Parse_Block_LAS_Arg(argv[2]);
if (! Next_Block_Exists(parse))
{ ISTWO = 1;
status = Open_DB(argv[2],db2);
if (status < 0)
exit (1);
if (db2->part > 0)
{ fprintf(stderr,"%s: Cannot be called on a block: %s\n",Prog_Name,argv[2]);
exit (1);
}
Trim_DB(db2);
}
else
db2 = db1;
Free_Block_Arg(parse);
}
Trim_DB(db1);
}
{ char *iblock;
int64 bsize, ovlsize, ptrsize;
int i, j;
DAZZ_READ *reads1 = db1->reads;
int nreads1 = db1->nreads;
DAZZ_READ *reads2 = db2->reads;
int nreads2 = db2->nreads;
// Setup IO buffers
ptrsize = sizeof(void *);
ovlsize = sizeof(Overlap) - ptrsize;
bsize = MEMORY * 1000000ll;
iblock = (char *) Malloc(bsize+ptrsize,"Allocating input block");
if (iblock == NULL)
exit (1);
iblock += ptrsize;
// For each file do
status = 0;
for (i = 2+ISTWO; i < argc; i++)
{ Block_Looper *parse;
FILE *input;
char *disp;
char *iptr, *itop;
Overlap last, prev;
int64 novl;
int tspace, tbytes;
int has_chains;
// Establish IO and (novl,tspace) header
parse = Parse_Block_LAS_Arg(argv[i]);
while ((input = Next_Block_Arg(parse)) != NULL)
{ disp = Block_Arg_Root(parse);
if (fread(&novl,sizeof(int64),1,input) != 1)
SYSTEM_READ_ERROR
if (fread(&tspace,sizeof(int),1,input) != 1)
SYSTEM_READ_ERROR
if (novl < 0)
{ if (VERBOSE)
fprintf(stderr," %s: Number of alignments < 0\n",disp);
goto error;
}
if (tspace < 0)
{ if (VERBOSE)
fprintf(stderr," %s: Trace spacing < 0\n",disp);
goto error;
}
if (tspace <= TRACE_XOVR && tspace != 0)
tbytes = sizeof(uint8);
else
tbytes = sizeof(uint16);
iptr = iblock;
itop = iblock + fread(iblock,1,bsize,input);
// For each record in file do
has_chains = 0;
last.aread = -1;
last.bread = -1;
last.flags = 0;
last.path.bbpos = last.path.abpos = 0;
last.path.bepos = last.path.aepos = 0;
prev = last;
for (j = 0; j < novl; j++)
{ Overlap ovl;
int tsize;
int equal;
// Fetch next record
if (iptr + ovlsize > itop)
{ int64 remains = itop-iptr;
if (remains > 0)
memmove(iblock,iptr,remains);
iptr = iblock;
itop = iblock + remains;
itop += fread(itop,1,bsize-remains,input);
if (iptr + ovlsize > itop)
{ if (VERBOSE)
fprintf(stderr," %s: Too few alignment records\n",disp);
goto error;
}
}
ovl = *((Overlap *) (iptr - ptrsize));
iptr += ovlsize;
tsize = ovl.path.tlen*tbytes;
if (iptr + tsize > itop)
{ int64 remains = itop-iptr;
if (remains > 0)
memmove(iblock,iptr,remains);
iptr = iblock;
itop = iblock + remains;
itop += fread(itop,1,bsize-remains,input);
if (iptr + tsize > itop)
{ if (VERBOSE)
fprintf(stderr," %s: Too few alignment records\n",disp);
goto error;
}
}
ovl.path.trace = iptr;
iptr += tsize;
// Basic checks
if (ovl.aread < 0 || ovl.bread < 0)
{ if (VERBOSE)
fprintf(stderr," %s: Read indices < 0\n",disp);
goto error;
}
if (ovl.aread >= nreads1 || ovl.bread >= nreads2)
{ if (VERBOSE)
fprintf(stderr," %s: Read indices out of range\n",disp);
goto error;
}
if (ovl.path.abpos >= ovl.path.aepos || ovl.path.aepos > reads1[ovl.aread].rlen ||
ovl.path.bbpos >= ovl.path.bepos || ovl.path.bepos > reads2[ovl.bread].rlen ||
ovl.path.abpos < 0 || ovl.path.bbpos < 0 )
{ if (VERBOSE)
fprintf(stderr," %s: Non-sense alignment intervals\n",disp);
goto error;
}
if (ovl.path.diffs < 0 || ovl.path.diffs > reads1[ovl.aread].rlen ||
ovl.path.diffs > reads2[ovl.bread].rlen)
{ if (VERBOSE)
fprintf(stderr," %s: Non-sense number of differences\n",disp);
goto error;
}
if (Check_Trace_Points(&ovl,tspace,VERBOSE,disp))
goto error;
if (j == 0)
has_chains = ((ovl.flags & (START_FLAG | NEXT_FLAG | BEST_FLAG)) != 0);
if (has_chains)
{ if (CHAIN_START(ovl.flags) && CHAIN_NEXT(ovl.flags))
{ if (VERBOSE)
fprintf(stderr," %s: LA has both start & next flag set\n",disp);
goto error;
}
if (BEST_CHAIN(ovl.flags) && CHAIN_NEXT(ovl.flags))
{ if (VERBOSE)
fprintf(stderr," %s: LA has both best & next flag set\n",disp);
goto error;
}
}
else
{ if ((ovl.flags & (START_FLAG | NEXT_FLAG | BEST_FLAG)) != 0)
{ if (VERBOSE)
fprintf(stderr," %s: LAs should not have chain flags\n",disp);
goto error;
}
}
// Duplicate check and sort check if -S set
equal = 0;
if (SORTED)
{ if (CHAIN_NEXT(ovl.flags))
{ if (ovl.aread == last.aread && ovl.bread != last.bread &&
COMP(ovl.flags) != COMP(last.flags) &&
ovl.path.abpos >= last.path.abpos &&
ovl.path.bbpos >= last.path.bbpos)
goto dupcheck;
if (VERBOSE)
fprintf(stderr," %s: Chain is not valid (%d vs %d)\n",
disp,ovl.aread+1,ovl.bread+1);
goto error;
}
else if (!has_chains)
{ if (ovl.aread > last.aread) goto inorder;
if (ovl.aread == last.aread)
{ if (MAP_ORDER)
{ if (ovl.path.abpos > prev.path.abpos) goto inorder;
if (ovl.path.abpos == prev.path.abpos)
goto dupcheck;
}
else
{ if (ovl.bread > last.bread) goto inorder;
if (ovl.bread == last.bread)
{ if (COMP(ovl.flags) > COMP(last.flags)) goto inorder;
if (COMP(ovl.flags) == COMP(last.flags))
{ if (ovl.path.abpos > last.path.abpos) goto inorder;
if (ovl.path.abpos == last.path.abpos)
{ equal = 1;
goto inorder;
}
}
}
}
}
if (VERBOSE)
fprintf(stderr," %s: LAs are not sorted (%d vs %d)\n",
disp,ovl.aread+1,ovl.bread+1);
goto error;
}
else // First element of a chain
{ if (ovl.aread > prev.aread) goto inorder;
if (ovl.aread == prev.aread)
{ if (MAP_ORDER)
{ if (ovl.path.abpos > prev.path.abpos) goto inorder;
if (ovl.path.abpos == prev.path.abpos)
goto dupcheck;
}
else
{ if (ovl.bread > prev.bread) goto inorder;
if (ovl.bread == prev.bread)
{ if (COMP(ovl.flags) > COMP(prev.flags)) goto inorder;
if (COMP(ovl.flags) == COMP(prev.flags))
{ if (ovl.path.abpos > prev.path.abpos) goto inorder;
if (ovl.path.abpos == prev.path.abpos)
{ equal = 1;
goto dupcheck;
}
}
}
}
}
if (VERBOSE)
fprintf(stderr," %s: Chains are not sorted (%d vs %d)\n",
disp,ovl.aread+1,ovl.bread+1);
goto error;
}
}
dupcheck:
if (ovl.aread == last.aread && ovl.bread == last.bread &&
COMP(ovl.flags) == COMP(last.flags) && ovl.path.abpos == last.path.abpos)
equal = 1;
inorder:
if (equal)
{ if (ovl.path.aepos == last.path.aepos &&
ovl.path.bbpos == last.path.bbpos &&
ovl.path.bepos == last.path.bepos)
{ if (VERBOSE)
fprintf(stderr," %s: Duplicate LAs (%d vs %d)\n",
disp,ovl.aread+1,ovl.bread+1);
goto error;
}
}
last = ovl;
if (CHAIN_START(ovl.flags))
prev = ovl;
}
// File processing epilog: Check all data read and print OK if -v
if (iptr < itop)
{ if (VERBOSE)
fprintf(stderr," %s: Too many alignment records\n",disp);
goto error;
}
if (VERBOSE)
{ printf(" %s: ",disp);
Print_Number(novl,0,stdout);
printf(" all OK\n");
fflush(stdout);
}
goto cleanup;
error:
status = 1;
if (VERBOSE)
{ printf(" %s: Not OK, see stderr\n",disp);
fflush(stdout);
}
cleanup:
if (input != NULL)
fclose(input);
}
Free_Block_Arg(parse);
}
free(iblock-ptrsize);
}
Close_DB(db1);
if (ISTWO)
Close_DB(db2);
exit (status);
}