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#include <stdio.h>
#include <stdlib.h>
#include <string.h>
#include <errno.h>
#include "bio++.H"
#include "existDB.H"
#include "libmeryl.H"
#include "seqCache.H"
#include "seqStream.H"
#include "merStream.H"
// Driver for the existDB creation. Reads a sequence.fasta, builds
// an existDB for the mers in the file, and then writes the internal
// structures to disk.
//
// The existDB constructor is smart enough to read either a pre-built
// image or a regular multi-fasta file.
int
testFiles(char *filename, char *prefix, uint32 merSize) {
char *prefixfilename = new char [strlen(prefix) + 32];
// Create existDB e and save it to disk
//
existDB *e = new existDB(filename, merSize, existDBnoFlags | existDBcounts, 0, ~uint32ZERO);
sprintf(prefixfilename, "%s.1", prefix);
e->saveState(prefixfilename);
// Create existDB f by loading the saved copy from disk
//
existDB *f = new existDB(prefixfilename);
// Create a fresh existDB g (to check if we corrup the original when saved)
//
existDB *g = new existDB(filename, merSize, existDBnoFlags | existDBcounts, 0, ~uint32ZERO);
speedCounter *C = new speedCounter(" %7.2f Mmers -- %5.2f Mmers/second\r", 1000000.0, 0x1fffff, true);
fprintf(stderr, "Need to iterate over %7.2f Mmers.\n", (uint64MASK(2 * merSize) + 1) / 1000000.0);
for (uint64 d=0, m=uint64MASK(2 * merSize); m--; ) {
bool ee = e->exists(m);
bool ef = f->exists(m);
bool eg = g->exists(m);
uint32 ce = e->count(m);
uint32 cf = f->count(m);
uint32 cg = g->count(m);
if ((ee != ef) || (ef != eg) || (ee != eg))
fprintf(stderr, "mer "uint64HEX" not found : e=%d f=%d g=%d\n", m, ee, ef, eg);
if ((ce != cf) || (cf != cg) || (ce != cg))
fprintf(stderr, "mer "uint64HEX" count differs : e=%u f=%u g=%u (exists=%d)\n", m, ce, cf, cg, ee);
if ((m & 0xffffff) == 0) {
// Been a while since a report, so report.
d = 1;
}
if ((ce > 1) && (d == 1)) {
// Report anything not unique, to make sure that we're testing real counts and not just existence.
fprintf(stderr, "mer "uint64HEX" : e=%u f=%u g=%u (exists=%d)\n", m, ce, cf, cg, ee);
d = 0;
}
C->tick();
}
delete e;
delete C;
return(0);
}
int
testExistence(char *filename, uint32 merSize) {
existDB *E = new existDB(filename, merSize, existDBnoFlags, 0, ~uint32ZERO);
merStream *M = new merStream(new kMerBuilder(merSize), new seqStream(filename), true, true);
uint64 tried = 0;
uint64 lost = 0;
while (M->nextMer()) {
tried++;
if (!E->exists(M->theFMer()))
lost++;
}
delete M;
delete E;
if (lost) {
fprintf(stderr, "Tried "uint64FMT", didn't find "uint64FMT" merStream mers in the existDB.\n", tried, lost);
return(1);
} else {
return(0);
}
}
int
testExhaustive(char *filename, char *merylname, uint32 merSize) {
existDB *E = new existDB(filename, merSize, existDBnoFlags, 0, ~uint32ZERO);
merylStreamReader *M = new merylStreamReader(merylname);
speedCounter *C = new speedCounter(" %7.2f Mmers -- %5.2f Mmers/second\r", 1000000.0, 0x1fffff, true);
uint64 found = uint64ZERO;
uint64 expected = uint64ZERO;
FILE *DUMP = 0L;
DUMP = fopen("testExhaustive.ms.dump", "w");
while (M->nextMer()) {
if (E->exists(M->theFMer())) {
expected++;
fprintf(DUMP, uint64HEX"\n", (uint64)M->theFMer());
} else {
fprintf(DUMP, uint64HEX" MISSED!\n", (uint64)M->theFMer());
}
}
fclose(DUMP);
fprintf(stderr, "Found "uint64FMT" mers in the meryl database.\n", expected);
fprintf(stderr, "Need to iterate over %7.2f Mmers.\n", (uint64MASK(2 * merSize) + 1) / 1000000.0);
DUMP = fopen("testExhaustive.ck.dump", "w");
for (uint64 m = uint64MASK(2 * merSize); m--; ) {
if (E->exists(m)) {
found++;
fprintf(DUMP, uint64HEX"\n", m);
}
C->tick();
}
fclose(DUMP);
delete C;
delete E;
delete M;
if (expected != found) {
fprintf(stderr, "Expected to find "uint64FMT" mers, but found "uint64FMT" instead.\n",
expected, found);
return(1);
} else {
return(0);
}
}
const char *usage =
"usage: %s [stuff]\n"
" -mersize mersize\n"
" -- Use the specified mersize when building existDB tables.\n"
"\n"
" -build some.fasta prefix\n"
" -- Build an existDB on all mers in some.fasta and save\n"
" the tables into prefix.\n"
"\n"
" -describe prefix\n"
" -- Reports the state of some existDB file.\n"
"\n"
" -testfiles some.fasta prefix\n"
" -- Build an existDB table from some.fasta. Write that table to disk.\n"
" Load the table back. Compare that each mer in some.fasta is present\n"
" in all three existDB tables created earlier.\n"
"\n"
" -testexistence some.fasta\n"
" -- Build an existDB table from some.fasta, check that every\n"
" mer in some.fasta can be found in the table. Does not\n"
" guarantee that every mer in the table is found in the file.\n"
"\n"
" -testexhaustive some.fasta some.meryl\n"
" -- Build an existDB table from some.fasta, check _EVERY_ mer\n"
" for existence. Complain if a mer exists in the table but\n"
" not in the meryl database. Assumes 'some.meryl' is the\n"
" mercount of some.fasta.\n"
"\n";
int
main(int argc, char **argv) {
uint32 mersize = 20;
if (argc < 3) {
fprintf(stderr, usage, argv[0]);
exit(1);
}
int arg = 1;
while (arg < argc) {
if (strncmp(argv[arg], "-mersize", 2) == 0) {
arg++;
mersize = atoi(argv[arg]);
} else if (strncmp(argv[arg], "-describe", 2) == 0) {
existDB *e = new existDB(argv[argc-1], false);
e->printState(stdout);
delete e;
exit(0);
} else if (strncmp(argv[arg], "-testfiles", 8) == 0) {
exit(testFiles(argv[arg+1], argv[arg+2], mersize));
} else if (strncmp(argv[arg], "-testexistence", 8) == 0) {
exit(testExistence(argv[arg+1], mersize));
} else if (strncmp(argv[arg], "-testexhaustive", 8) == 0) {
exit(testExhaustive(argv[arg+1], argv[arg+2], mersize));
} else if (strncmp(argv[arg], "-build", 2) == 0) {
existDB *e = new existDB(argv[argc-2], mersize, existDBnoFlags, 0, ~uint32ZERO);
e->saveState(argv[argc-1]);
delete e;
exit(0);
}
arg++;
}
exit(0);
}
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