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HPC.DAScover.c
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HPC.DAScover.c
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/*********************************************************************************************\
*
* HPC script to update coverage statistics upon an update to the database
*
* Produce a script to
* 1. create low complexity mask for the given DB (DBdust)
* 2. create tandem repeat mask for the given DB (datander + TANmask)
* 3. create overlap based repeat mask for the given DB,
* based on diagonal blocks N vs N (daligner + REPmask)
* 4. compute overlaps for block 1 of pairs of a DB, and then sort and merge them
* into as many .las files as their are blocks. Run DAScover on the resulting .las files
*
*
* Author: Martin Pippel, Gene Myers
* Date : March 19, 2018
*
*********************************************************************************************/
#include <stdio.h>
#include <stdlib.h>
#include <string.h>
#include <math.h>
#include <ctype.h>
#include <unistd.h>
#include <sys/types.h>
#include <sys/stat.h>
#include "DB.h"
static char *Usage[] =
{ "[-vlF] [-U(w<int(64)> |t<double(2.)> |m<int(10)> |b) ]",
" [-S(k<int(12)> |w<int(4)> |h<int(35)> |e<double(.7)> |l<int(500)>) ]",
" [-L(k<int(14)> |w<int(6)> |h<int(35)> |e<double(.7)> |l<int(1000)> |t<int>) ]",
" [-c<int(10)>] [-s<int(100)] [-M<int>] [-P<dir(/tmp)>] [-T<int(4)>]",
" [-B<int(4)>] [-f<name>] <reads:db|dam> [<target:int(1)>]"
};
int main(int argc, char *argv[])
{ int nblocks;
int usepath;
int fblock, lblock, tblock;
char *pwd, *root;
int VERBOSE; // Option parameters
int ALLBLKS;
int FORCE;
int BLOCKID;
char *PROJECT;
int BUNIT;
int COVERAGE;
int TRACE;
char *TMPDIR;
int NTHREADS;
int MEMORY;
int D_BIAS;
int D_WINDOW;
float D_THRESH;
int D_MINBP;
int S_KMER;
int S_BAND;
int S_HITS;
float S_ERATE;
int S_OLEN;
int D_KMER;
int D_BAND;
int D_HITS;
float D_ERATE;
int D_OLEN;
int D_FREQ;
{ int i, j, k; // Process options
int flags[128];
char *eptr;
ARG_INIT("HPC.DAScover")
BLOCKID = 1;
PROJECT = NULL;
BUNIT = 4;
COVERAGE = 10;
TRACE = 100;
TMPDIR = "/tmp";
NTHREADS = 4;
MEMORY = 16;
D_BIAS = 0;
D_WINDOW = 64;
D_THRESH = -1.;
D_MINBP = 10;
S_KMER = 12;
S_BAND = 4;
S_HITS = 35;
S_ERATE = 0.;
S_OLEN = 500;
D_FREQ = -1;
D_KMER = 14;
D_BAND = 6;
D_HITS = 35;
D_ERATE = 0.;
D_OLEN = 1000;
j = 1;
for (i = 1; i < argc; i++)
if (argv[i][0] == '-')
switch (argv[i][1])
{ default:
ARG_FLAGS("vlF")
break;
case 'c':
ARG_POSITIVE(COVERAGE, "Repeat coverage threshold")
break;
case 'f':
PROJECT = argv[i]+2;
break;
case 's':
ARG_POSITIVE(TRACE, "Trace spacing")
break;
case 'B':
ARG_POSITIVE(BUNIT, "Blocks per command")
break;
case 'M':
ARG_POSITIVE(MEMORY, "Daligner memory usage")
break;
case 'P':
TMPDIR = argv[i]+2;
break;
case 'T':
ARG_POSITIVE(NTHREADS, "Number of threads (daligner+datander)")
break;
case 'U':
argv[i] += 1;
switch (argv[i][1])
{ case 'b':
D_BIAS = 1;
break;
case 'm':
ARG_POSITIVE(D_MINBP, "DBdust minimum bases")
break;
case 'w':
ARG_POSITIVE(D_WINDOW, "DBdust window size")
break;
case 't':
ARG_REAL(D_THRESH)
break;
default:
fprintf(stderr, "%s: option '-%s' not supported for DBdust\n",
Prog_Name, argv[i]);
exit(1);
}
break;
case 'S':
argv[i] += 1;
switch (argv[i][1])
{ case 'e':
ARG_REAL(S_ERATE)
if (S_ERATE < .7 || S_ERATE >= 1.)
{ fprintf(stderr, "%s: Average correlation must be in [.7,1.) (%g)\n",
Prog_Name, S_ERATE);
exit(1);
}
break;
case 'h':
ARG_POSITIVE(S_HITS, "Datander hit threshold")
break;
case 'k':
ARG_POSITIVE(S_KMER, "Datander kmer")
break;
case 'l':
ARG_POSITIVE(S_OLEN, "Datander minimum alignment length")
break;
case 'w':
ARG_POSITIVE(S_BAND, "Datander band width")
break;
default:
fprintf(stderr, "%s: option '-%s' not supported for datander\n",
Prog_Name, argv[i]);
exit(1);
}
break;
case 'L':
argv[i] += 1;
switch (argv[i][1])
{ case 'e':
ARG_REAL(D_ERATE)
if (D_ERATE < .7 || D_ERATE >= 1.)
{ fprintf(stderr, "%s: Average correlation must be in [.7,1.) (%g)\n",
Prog_Name, D_ERATE);
exit(1);
}
break;
case 'h':
ARG_POSITIVE(D_HITS, "Daligner hit threshold")
break;
case 'k':
ARG_POSITIVE(D_KMER, "Daligner kmer")
break;
case 'l':
ARG_POSITIVE(D_OLEN, "Daligner minimum alignment length")
break;
case 't':
ARG_POSITIVE(D_FREQ, "Daligner tuple suppresion frequency")
break;
case 'w':
ARG_POSITIVE(D_BAND, "Daligner band width")
break;
default:
fprintf(stderr, "%s: option '-%s' not supported for daligner\n",
Prog_Name, argv[i]);
exit(1);
}
break;
}
else
argv[j++] = argv[i];
argc = j;
VERBOSE = flags['v'];
ALLBLKS = flags['l'];
FORCE = flags['F'];
if (argc < 2 || argc > 3)
{ fprintf(stderr,"Usage: %s %s\n",Prog_Name,Usage[0]);
fprintf(stderr," %*s %s\n",(int) strlen(Prog_Name),"",Usage[1]);
fprintf(stderr," %*s %s\n",(int) strlen(Prog_Name),"",Usage[2]);
fprintf(stderr," %*s %s\n",(int) strlen(Prog_Name),"",Usage[3]);
fprintf(stderr," %*s %s\n",(int) strlen(Prog_Name),"",Usage[4]);
fprintf(stderr,"\n");
fprintf(stderr, " Create an HPC workflow to estimate the coverage of a given DB:\n");
fprintf(stderr, " 1. Create low complexity mask for the given DB (DBdust)\n");
fprintf(stderr, " 2. Create tandem masks for each DB block (datander + TANmask)\n");
fprintf(stderr, " 3. Create repeat mask for each DB block by self-comparison");
fprintf(stderr, " (daligner + REPmask)\n");
fprintf(stderr, " 4. Compute all soft-masked overlaps for <target> block (default 1) vs");
fprintf(stderr, " all other DB blocks.\n");
fprintf(stderr, " 5. Run DAScover on the target block .las file\n");
fprintf(stderr,"\n");
fprintf(stderr," DBdust parameters.\n");
fprintf(stderr," -Uw: DUST algorithm window size.\n");
fprintf(stderr," -Ut: DUST algorithm threshold.\n");
fprintf(stderr," -Um: Record only low-complexity intervals >= this size.\n");
fprintf(stderr," -Ub: Take into account base composition bias.\n");
fprintf(stderr,"\n");
fprintf(stderr," Datander parameters.\n");
fprintf(stderr," -Sk: k-mer size (must be <= 32).\n");
fprintf(stderr," -Sw: Look for k-mers in averlapping bands of size 2^-w.\n");
fprintf(stderr," -Sh: A seed hit if the k-mers in band cover >= -h bps in the");
fprintf(stderr, " targest read.\n");
fprintf(stderr," -Se: Look for alignments with -e percent similarity.\n");
fprintf(stderr," -Sl: Look for alignments of length >= -l.\n");
fprintf(stderr,"\n");
fprintf(stderr," Daligner parameters.\n");
fprintf(stderr," -Lk: k-mer size (must be <= 32).\n");
fprintf(stderr," -Lw: Look for k-mers in averlapping bands of size 2^-w.\n");
fprintf(stderr," -Lh: A seed hit if the k-mers in band cover >= -h bps in the");
fprintf(stderr, " targest read.\n");
fprintf(stderr," -Le: Look for alignments with -e percent similarity.\n");
fprintf(stderr," -Ll: Look for alignments of length >= -l.\n");
fprintf(stderr," -Lt: Ignore k-mers that occur >= -t times in a block.\n");
fprintf(stderr,"\n");
fprintf(stderr," Common parameters.\n");
fprintf(stderr," -s: Use -s as the trace point spacing for encoding alignments");
fprintf(stderr, " (daligner, datander).\n");
fprintf(stderr," -M: Use only -M GB of memory by ignoring most frequent k-mers");
fprintf(stderr, " (daligner.\n");
fprintf(stderr," -P: Use this directory for all scratch files");
fprintf(stderr, " (daligner, datander, LAsort, LAmerge).\n");
fprintf(stderr," -T: Use -T threads (daligner, datander).\n");
fprintf(stderr,"\n");
fprintf(stderr," Script control.\n");
fprintf(stderr," -v: Run all commands in script in verbose mode.\n");
fprintf(stderr," -f: Place script bundles in separate files with prefix <name>\n");
fprintf(stderr," -l: Include the last block in the calculation\n");
fprintf(stderr," -B: # of block compares per command job\n");
fprintf(stderr," -F: Restart computation from the beginnning\n");
exit (1);
}
}
// Make sure DB exists and is partitioned, get number of blocks in partition
pwd = PathTo(argv[1]);
if (strcmp(argv[1] + (strlen(argv[1]) - 4), ".dam") == 0)
{ fprintf(stderr, "\n%s: A mapper database (.dam) is not supported!\n\n", Prog_Name);
exit(1);
}
root = Root(argv[1], ".db");
{ int i, nfiles;
FILE *dbvis;
dbvis = Fopen(Catenate(pwd, "/", root, ".db"), "r");
if (dbvis == NULL)
exit(1);
if (fscanf(dbvis, "files = %d\n", &nfiles) != 1)
SYSTEM_READ_ERROR
for (i = 0; i < nfiles; i++)
{ char buffer[30001];
if (fgets(buffer, 30000, dbvis) == NULL)
SYSTEM_READ_ERROR
}
if (fscanf(dbvis, "blocks = %d\n", &nblocks) != 1)
{ fprintf(stderr,"%s: Database must be split!\n",Prog_Name);
exit (1);
}
usepath = (strcmp(pwd, ".") != 0);
fclose(dbvis);
}
if (argc == 3)
{ char *eptr;
BLOCKID = strtol(argv[2],&eptr,10);
if (*eptr != '\0')
{ fprintf(stderr,"%s: target block '%s' should be an integer\n",Prog_Name,argv[2]);
exit (1);
}
}
if (BLOCKID > (nblocks-1) + ALLBLKS)
{ fprintf(stderr,"%s: Target block %d is greater than # of%sblocks in the db (%d)!\n",
Prog_Name, BLOCKID, ALLBLKS ?" ":" complete ", (nblocks-1)+ALLBLKS);
exit(1);
}
// determine which blocks are new
{ char *tail;
int i;
if (ALLBLKS)
lblock = nblocks;
else
lblock = nblocks-1;
if (lblock <= 0)
{ fprintf(stderr,"%s: DB has 1 block, if its complete use -l\n",Prog_Name);
exit (1);
}
tail = Strdup(Numbered_Suffix(".",BLOCKID,".las"),"Creating .las string");
for (i = nblocks; i >= 1; i--)
if (access(Numbered_Suffix(Catenate(pwd,"/",root,"."),i,tail),F_OK) == 0)
break;
tblock = i;
free(tail);
if ( ! FORCE && tblock >= lblock)
{ fprintf(stderr,"%s: Nothing to do!\n",Prog_Name);
exit (1);
}
fblock = 1;
if ( ! FORCE)
{ for (i = 1; i <= nblocks; i++)
{ if (access(Numbered_Suffix(Catenate(pwd, "/.", root, "."), i, ".dust.anno"),F_OK) < 0)
break;
if (access(Numbered_Suffix(Catenate(pwd, "/.", root, "."), i, ".tan.anno"),F_OK) < 0)
break;
if (access(Numbered_Suffix(Catenate(pwd, "/.", root, "."), i, ".rep.anno"),F_OK) < 0)
break;
}
fblock = i;
}
if (VERBOSE)
{ fprintf(stderr,"# Masking blocks %d-%d, add blocks from %d to target .las\n",
fblock,lblock,tblock+1);
}
}
{ FILE *out;
char name[1000];
int njobs;
int i, j, k;
// CREATE BLOCK MASKS
if (fblock <= lblock)
{
// 01 create low complexity (dust) track
if (PROJECT != NULL)
{ sprintf(name, "%s.01.DUST", PROJECT);
out = fopen(name, "w");
}
else
out = stdout;
njobs = (lblock - fblock) + 1;
if (VERBOSE)
fprintf(stderr, "# 01 DBdust - jobs (%d)\n", njobs);
for (i = fblock; i <= lblock; i++)
{ fprintf(out, "DBdust");
if (D_BIAS)
fprintf(out, " -b");
if (D_WINDOW != 64)
fprintf(out, " -w%d", D_WINDOW);
if (D_THRESH >= 0.)
fprintf(out, " -t%.2f", D_THRESH);
if (D_MINBP != 10)
fprintf(out, " -m%d", D_MINBP);
if (usepath)
fprintf(out, " %s/%s.%d", pwd, root, i);
else
fprintf(out, " %s.%d", root, i);
fprintf(out, "\n");
}
// 02 create tandem repeat (tan) track - step 1 datander
if (PROJECT != NULL)
{ fclose(out);
sprintf(name, "%s.02.TANDEM", PROJECT);
out = fopen(name, "w");
}
njobs = (lblock - fblock) / BUNIT + 1;
if (VERBOSE)
fprintf(stderr, "# 02 Datander - jobs (%d)\n", njobs);
for (i = fblock; i <= lblock; i = j)
{ j = i + BUNIT;
if (j > lblock + 1)
j = lblock + 1;
fprintf(out, "datander");
if (VERBOSE)
fprintf(out, " -v");
if (S_KMER != 12)
fprintf(out, " -k%d", S_KMER);
if (S_BAND != 4)
fprintf(out, " -w%d", S_BAND);
if (S_HITS != 35)
fprintf(out, " -h%d", S_HITS);
if (S_ERATE > 0.)
fprintf(out, " -e%g", S_ERATE);
if (S_OLEN != 500)
fprintf(out, " -l%d", S_OLEN);
if (TRACE != 100)
fprintf(out, " -s%d", TRACE);
if (strcmp(TMPDIR, "/tmp"))
fprintf(out, " -P%s", TMPDIR);
if (NTHREADS != 4)
fprintf(out, " -T%d", NTHREADS);
for (k = i; k < j; k++)
if (usepath)
fprintf(out, " %s/%s.%d", pwd, root, k);
else
fprintf(out, " %s.%d", root, k);
fprintf(out, "\n");
}
// 03 create tandem repeat (tan) track - step 2 check datander
if (VERBOSE)
fprintf(stderr, "# 03 Check all TAN.*.las - jobs (%d)\n", njobs);
if (PROJECT != NULL)
{ fclose(out);
sprintf(name, "%s.03.CHECK.TAN", PROJECT);
out = fopen(name, "w");
}
for (i = fblock; i <= lblock; i = j)
{ j = i + BUNIT;
if (j > lblock + 1)
j = lblock + 1;
fprintf(out, "LAcheck -S");
if (VERBOSE)
fprintf(out, " -v");
if (usepath)
fprintf(out, " %s/%s", pwd, root);
else
fprintf(out, " %s", root);
fprintf(out, " TAN.%s.@%d-%d", root, i, j - 1);
fprintf(out, "\n");
}
// 04 create tandem repeat (tan) track - step 3 TANmask
if (VERBOSE)
fprintf(stderr, "# 04 TANmask - jobs (%d)\n", njobs);
if (PROJECT != NULL)
{ fclose(out);
sprintf(name, "%s.04.TANMASK", PROJECT);
out = fopen(name, "w");
}
for (i = fblock; i <= lblock; i = j)
{ j = i + BUNIT;
if (j > lblock + 1)
j = lblock + 1;
fprintf(out, "TANmask");
if (VERBOSE)
fprintf(out, " -v");
if (S_OLEN != 500)
fprintf(out, " -l%d", S_OLEN);
if (usepath)
fprintf(out, " %s/%s", pwd, root);
else
fprintf(out, " %s", root);
fprintf(out, " TAN.%s.@%d-%d", root, i, j - 1);
fprintf(out, "\n");
}
// 05 create tandem repeat (tan) track - step 4 remove .las files
if (VERBOSE)
fprintf(stderr, "# 05 Remove all TAN.*.las jobs (%d)\n", njobs);
if (PROJECT != NULL)
{ fclose(out);
sprintf(name, "%s.05.RM.TAN", PROJECT);
out = fopen(name, "w");
}
for (i = fblock; i <= lblock; i = j)
{ j = i + BUNIT;
if (j > lblock + 1)
j = lblock + 1;
fprintf(out, "rm");
for (k = i; k < j; k++)
fprintf(out, " TAN.%s.%d.las", root, k);
fprintf(out, "\n");
}
// REPEAT MASKING
// 06 create overlap based repeat (rep) track - step 1 daligner
njobs = (lblock - fblock) + 1;
if (VERBOSE)
fprintf(stderr, "# 06 Repeat Masking: Daligner - jobs (%d)\n", njobs);
if (PROJECT != NULL)
{ fclose(out);
sprintf(name, "%s.06.REPEAT", PROJECT);
out = fopen(name, "w");
}
for (i = fblock; i <= lblock; i++)
{ fprintf(out, "daligner");
if (VERBOSE)
fprintf(out, " -v");
if (D_KMER != 14)
fprintf(out, " -k%d", D_KMER);
if (D_BAND != 6)
fprintf(out, " -w%d", D_BAND);
if (D_HITS != 35)
fprintf(out, " -h%d", D_HITS);
if (D_ERATE > 0.)
fprintf(out, " -e%g", D_ERATE);
if (D_OLEN != 1000)
fprintf(out, " -l%d", D_OLEN);
if (TRACE != 100)
fprintf(out, " -s%d", TRACE);
if (strcmp(TMPDIR, "/tmp"))
fprintf(out, " -P%s", TMPDIR);
if (NTHREADS != 4)
fprintf(out, " -T%d", NTHREADS);
fprintf(out, " -mdust -mtan"); // add dust and tan track
if (usepath)
fprintf(out, " %s/%s.%d %s/%s.%d", pwd, root, i, pwd, root, i);
else
fprintf(out, " %s.%d %s.%d", root, i, root, i);
fprintf(out, "\n");
}
// 07 create overlap based repeat (rep) track - step 2 check .las files
njobs = (lblock - fblock) / BUNIT + 1;
if (VERBOSE)
fprintf(stderr, "# 07 Repeat Masking: Check all .las - jobs (%d) \n", njobs);
if (PROJECT != NULL)
{ fclose(out);
sprintf(name, "%s.07.CHECK.REP", PROJECT);
out = fopen(name, "w");
}
for (i = fblock; i <= lblock; i = j)
{ j = i + BUNIT;
if (j > lblock + 1)
j = lblock + 1;
fprintf(out, "LAcheck -S");
if (VERBOSE)
fprintf(out, " -v");
if (usepath)
fprintf(out, " %s/%s", pwd, root);
else
fprintf(out, " %s", root);
for (k = i; k < j; k++)
fprintf(out, " %s.%d.%s.%d", root, k, root, k);
fprintf(out, "\n");
}
// 08 create overlap based repeat (rep) track - step 3 TANmask
if (PROJECT != NULL)
{ fclose(out);
sprintf(name, "%s.08.REPMASK", PROJECT);
out = fopen(name, "w");
}
if (VERBOSE)
fprintf(stderr, "# 08 Repeat masking: REPmask - jobs (%d)\n", njobs);
for (i = fblock; i <= lblock; i = j)
{ j = i + BUNIT;
if (j > lblock + 1)
j = lblock + 1;
fprintf(out, "REPmask -c%d", COVERAGE);
if (VERBOSE)
fprintf(out, " -v");
if (usepath)
fprintf(out, " %s/%s", pwd, root);
else
fprintf(out, " %s", root);
for (k = i; k < j; k++)
fprintf(out, " %s.%d.%s.%d", root, k, root, k);
fprintf(out, "\n");
}
// 09 create overlap based repeat (rep) track - step 4 remove .las files
if (VERBOSE)
fprintf(stderr, "# 09 Repeat masking: Remove .las files\n");
if (PROJECT != NULL)
{ fclose(out);
sprintf(name, "%s.09.RM.REP", PROJECT);
out = fopen(name, "w");
}
for (i = fblock; i <= lblock; i = j)
{ j = i + BUNIT;
if (j > lblock + 1)
j = lblock + 1;
fprintf(out, "rm");
for (k = i; k < j; k++)
fprintf(out, " %s.%d.%s.%d.las", root, k, root, k);
fprintf(out, "\n");
}
if (FORCE && tblock >= 1)
{ fprintf(out, "rm %s.%d.%d.las\n", root, tblock, BLOCKID);
tblock = 0;
}
}
// DASCOVER PROPER
njobs = (lblock - (tblock+1)) / BUNIT + 1;
if (VERBOSE)
fprintf(stderr, "# 10 DAScover: daligner - jobs (%d)\n", njobs);
if (PROJECT != NULL)
{ fclose(out);
sprintf(name, "%s.10.DALIGNER", PROJECT);
out = fopen(name, "w");
}
for (i = tblock+(BLOCKID <= tblock); i <= lblock; i = j)
{ if (i == tblock)
j = tblock+1;
else
{ j = i + BUNIT;
if (j > lblock + 1)
j = lblock + 1;
if (j == i+1 && i == BLOCKID)
continue;
}
fprintf(out, "daligner -mdust -mtan -mrep");
if (VERBOSE)
fprintf(out, " -v");
if (D_KMER != 14)
fprintf(out, " -k%d", D_KMER);
if (D_BAND != 6)
fprintf(out, " -w%d", D_BAND);
if (D_HITS != 35)
fprintf(out, " -h%d", D_HITS);
if (D_ERATE > 0.)
fprintf(out, " -e%g", D_ERATE);
if (D_OLEN != 1000)
fprintf(out, " -l%d", D_OLEN);
if (D_FREQ > 0)
fprintf(out, " -t%d", D_FREQ);
if (TRACE != 100)
fprintf(out, " -s%d", TRACE);
if (strcmp(TMPDIR, "/tmp"))
fprintf(out, " -P%s", TMPDIR);
if (NTHREADS != 4)
fprintf(out, " -T%d", NTHREADS);
if (i != tblock)
fprintf(out," -A");
if (usepath)
fprintf(out, " %s/%s.%d", pwd, root, BLOCKID);
else
fprintf(out, " %s.%d", root, BLOCKID);
for (k = i; k < j; k++)
{ if (k == BLOCKID)
continue;
if (i == tblock)
k = BLOCKID;
if (usepath)
fprintf(out, " %s/%s.%d", pwd, root, k);
else
fprintf(out, " %s.%d", root, k);
}
fprintf(out, "\n");
}
// Check .las files (optional)
if (VERBOSE)
fprintf(stderr, "# 11 DAScover: Check new .las files - jobs (%d)\n", njobs);
if (PROJECT != NULL)
{ fclose(out);
sprintf(name, "%s.11.CHECK.DAL", PROJECT);
out = fopen(name, "w");
}
for (i = tblock+1; i <= lblock; i = j)
{ j = i + BUNIT;
if (j > lblock + 1)
j = lblock + 1;
fprintf(out, "LAcheck -S");
if (VERBOSE)
fprintf(out, " -v");
if (usepath)
fprintf(out, " %s/%s", pwd, root);
else
fprintf(out, " %s", root);
fprintf(out, " %s.%d.%s.@%d-%d", root, BLOCKID, root, i, j - 1);
fprintf(out, "\n");
}
// LAmerge
if (VERBOSE)
fprintf(stderr, "# 12 DAScover: LAmerge final .las\n");
if (PROJECT != NULL)
{ fclose(out);
sprintf(name, "%s.12.MERGE", PROJECT);
out = fopen(name, "w");
}
fprintf(out, "LAmerge");
if (VERBOSE)
fprintf(out, " -v");
if (usepath)
fprintf(out, " %s/%s.%d.%d", pwd, root, lblock, BLOCKID);
else
fprintf(out, " %s.%d.%d", root, lblock, BLOCKID);
if (tblock >= 1)
{ if (usepath)
fprintf(out, " %s/%s.%d.%d", pwd, root, tblock, BLOCKID);
else
fprintf(out, " %s.%d.%d", root, tblock, BLOCKID);
}
fprintf(out, " %s.%d.%s.@%d-%d", root, BLOCKID, root, tblock+1, lblock);
fprintf(out, "\n");
// check final las file
if (VERBOSE)
fprintf(stderr, "# 13 DAScover: Check final merged .las\n");
if (PROJECT != NULL)
{ fclose(out);
sprintf(name, "%s.13.CHECK.MRG", PROJECT);
out = fopen(name, "w");
}
fprintf(out, "LAcheck -S");
if (VERBOSE)
fprintf(out, " -v");
if (usepath)
fprintf(out, " %s/%s %s/%s.%d.%d", pwd, root, pwd, root, lblock, BLOCKID);
else
fprintf(out, " %s %s.%d.%d", root, root, lblock, BLOCKID);
fprintf(out, "\n");
// 14 DAScover - step 4 remove DB.BLOCKID.DB.k.las files
if (VERBOSE)
fprintf(stderr, "# 14 DAScover: Remove intermediate .las files\n");
if (PROJECT != NULL)
{ fclose(out);
sprintf(name, "%s.14.RM.DAL", PROJECT);
out = fopen(name, "w");
}
if (tblock >= 1)
{ if (usepath)
printf("rm %s/%s.%d.%d.las\n",pwd,root,tblock,BLOCKID);
else
printf("rm %s.%d.%d.las\n",root,tblock,BLOCKID);
}
for (i = fblock; i <= lblock; i = j)
{ j = i + BUNIT;
if (j > lblock + 1)
j = lblock + 1;
fprintf(out, "rm");
for (k = i; k < j; k++)
fprintf(out, " %s.%d.%s.%d.las", root, BLOCKID, root, k);
fprintf(out, "\n");
}
// DAScover
if (VERBOSE)
fprintf(stderr, "# 15 DAScover\n");
if (PROJECT != NULL)
{ fclose(out);
sprintf(name, "%s.15.DASCOVER", PROJECT);
out = fopen(name, "w");
}
fprintf(out, "DAScover -v");
if (usepath)
fprintf(out, " %s/%s %s/%s.%d.%d.las", pwd, root, pwd, root, lblock, BLOCKID);
else
fprintf(out, " %s %s.%d.%d.las", root, root, lblock, BLOCKID);
fprintf(out, "\n");
if (PROJECT != NULL)
fclose(out);
}
exit (0);
}