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/*
* Copyright 2011, Ben Langmead <langmea@cs.jhu.edu>
*
* This file is part of Bowtie 2.
*
* Bowtie 2 is free software: you can redistribute it and/or modify
* it under the terms of the GNU General Public License as published by
* the Free Software Foundation, either version 3 of the License, or
* (at your option) any later version.
*
* Bowtie 2 is distributed in the hope that it will be useful,
* but WITHOUT ANY WARRANTY; without even the implied warranty of
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
* GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License
* along with Bowtie 2. If not, see <http://www.gnu.org/licenses/>.
*/
#include <mutex>
#include "aligner_cache.h"
#ifndef NDEBUG
/**
* Check that this QVal is internally consistent and consistent
* with the contents of the given cache.
*/
bool QVal::repOk(const AlignmentCache& ac) const {
if(rangen_ > 0) {
assert_lt(i_, ac.qSize());
assert_leq(i_ + rangen_, ac.qSize());
}
assert_geq(eltn_, rangen_);
return true;
}
#endif
#ifndef NDEBUG
/**
* Check that this SAVal is internally consistent and consistent
* with the contents of the given cache.
*/
bool SAVal::repOk(const AlignmentCache& ac) const {
assert(len == 0 || i < ac.saSize());
assert_leq(i + len, ac.saSize());
return true;
}
#endif
/**
* Add a new association between a read sequnce ('seq') and a
* reference sequence ('')
*/
bool AlignmentCache::addOnTheFlyImpl(
QVal& qv, // qval that points to the range of reference substrings
const SAKey& sak, // the key holding the reference substring
TIndexOffU topf, // top range elt in BWT index
TIndexOffU botf, // bottom range elt in BWT index
TIndexOffU topb, // top range elt in BWT' index
TIndexOffU botb) // bottom range elt in BWT' index
{
bool added = true;
// If this is the first reference sequence we're associating with
// the query sequence, initialize the QVal.
if(!qv.valid()) {
qv.init((uint32_t)qlist_.size(), 0, 0);
}
qv.addRange(botf-topf); // update tally for # ranges and # elts
if(!qlist_.add(pool(), sak)) {
return false; // Exhausted pool memory
}
#ifndef NDEBUG
for(size_t i = qv.offset(); i < qlist_.size(); i++) {
if(i > qv.offset()) {
assert(qlist_.get(i) != qlist_.get(i-1));
}
}
#endif
assert_eq(qv.offset() + qv.numRanges(), qlist_.size());
SANode *s = samap_.add(pool(), sak, &added);
if(s == NULL) {
return false; // Exhausted pool memory
}
assert(s->key.repOk());
if(added) {
s->payload.i = (TIndexOffU)salist_.size();
s->payload.len = botf - topf;
s->payload.topf = topf;
s->payload.topb = topb;
for(size_t j = 0; j < (botf-topf); j++) {
if(!salist_.add(pool(), OFF_MASK)) {
// Change the payload's len field
s->payload.len = (TIndexOffU)j;
return false; // Exhausted pool memory
}
}
assert(s->payload.repOk(*this));
}
// Now that we know all allocations have succeeded, we can do a few final
// updates
return true;
}
bool AlignmentCache::addOnTheFly(
QVal& qv, // qval that points to the range of reference substrings
const SAKey& sak, // the key holding the reference substring
TIndexOffU topf, // top range elt in BWT index
TIndexOffU botf, // bottom range elt in BWT index
TIndexOffU topb, // top range elt in BWT' index
TIndexOffU botb, // bottom range elt in BWT' index
bool getLock)
{
if(shared_ && getLock) {
ThreadSafe ts(mutex_m);
return addOnTheFlyImpl(qv, sak, topf, botf, topb, botb);
} else {
return addOnTheFlyImpl(qv, sak, topf, botf, topb, botb);
}
}
#ifdef ALIGNER_CACHE_MAIN
#include <iostream>
#include <getopt.h>
#include <string>
#include "random_source.h"
using namespace std;
enum {
ARG_TESTS = 256
};
static const char *short_opts = "vCt";
static struct option long_opts[] = {
{(char*)"verbose", no_argument, 0, 'v'},
{(char*)"tests", no_argument, 0, ARG_TESTS},
};
static void printUsage(ostream& os) {
os << "Usage: bowtie2-cache [options]*" << endl;
os << "Options:" << endl;
os << " --tests run unit tests" << endl;
os << " -v/--verbose talkative mode" << endl;
}
int gVerbose = 0;
static void add(
RedBlack<QKey, QVal>& t,
Pool& p,
const char *dna)
{
QKey qk;
qk.init(BTDnaString(dna, true));
t.add(p, qk, NULL);
}
/**
* Small tests for the AlignmentCache.
*/
static void aligner_cache_tests() {
RedBlack<QKey, QVal> rb(1024);
Pool p(64 * 1024, 1024);
// Small test
add(rb, p, "ACGTCGATCGT");
add(rb, p, "ACATCGATCGT");
add(rb, p, "ACGACGATCGT");
add(rb, p, "ACGTAGATCGT");
add(rb, p, "ACGTCAATCGT");
add(rb, p, "ACGTCGCTCGT");
add(rb, p, "ACGTCGAACGT");
assert_eq(7, rb.size());
rb.clear();
p.clear();
// Another small test
add(rb, p, "ACGTCGATCGT");
add(rb, p, "CCGTCGATCGT");
add(rb, p, "TCGTCGATCGT");
add(rb, p, "GCGTCGATCGT");
add(rb, p, "AAGTCGATCGT");
assert_eq(5, rb.size());
rb.clear();
p.clear();
// Regression test (attempt to make it smaller)
add(rb, p, "CCTA");
add(rb, p, "AGAA");
add(rb, p, "TCTA");
add(rb, p, "GATC");
add(rb, p, "CTGC");
add(rb, p, "TTGC");
add(rb, p, "GCCG");
add(rb, p, "GGAT");
rb.clear();
p.clear();
// Regression test
add(rb, p, "CCTA");
add(rb, p, "AGAA");
add(rb, p, "TCTA");
add(rb, p, "GATC");
add(rb, p, "CTGC");
add(rb, p, "CATC");
add(rb, p, "CAAA");
add(rb, p, "CTAT");
add(rb, p, "CTCA");
add(rb, p, "TTGC");
add(rb, p, "GCCG");
add(rb, p, "GGAT");
assert_eq(12, rb.size());
rb.clear();
p.clear();
// Larger random test
EList<BTDnaString> strs;
char buf[5];
for(int i = 0; i < 4; i++) {
for(int j = 0; j < 4; j++) {
for(int k = 0; k < 4; k++) {
for(int m = 0; m < 4; m++) {
buf[0] = "ACGT"[i];
buf[1] = "ACGT"[j];
buf[2] = "ACGT"[k];
buf[3] = "ACGT"[m];
buf[4] = '\0';
strs.push_back(BTDnaString(buf, true));
}
}
}
}
// Add all of the 4-mers in several different random orders
RandomSource rand;
for(unsigned runs = 0; runs < 100; runs++) {
rb.clear();
p.clear();
assert_eq(0, rb.size());
rand.init(runs);
EList<bool> used;
used.resize(256);
for(int i = 0; i < 256; i++) used[i] = false;
for(int i = 0; i < 256; i++) {
int r = rand.nextU32() % (256-i);
int unused = 0;
bool added = false;
for(int j = 0; j < 256; j++) {
if(!used[j] && unused == r) {
used[j] = true;
QKey qk;
qk.init(strs[j]);
rb.add(p, qk, NULL);
added = true;
break;
}
if(!used[j]) unused++;
}
assert(added);
}
}
}
/**
* A way of feeding simply tests to the seed alignment infrastructure.
*/
int main(int argc, char **argv) {
int option_index = 0;
int next_option;
do {
next_option = getopt_long(argc, argv, short_opts, long_opts, &option_index);
switch (next_option) {
case 'v': gVerbose = true; break;
case ARG_TESTS: aligner_cache_tests(); return 0;
case -1: break;
default: {
cerr << "Unknown option: " << (char)next_option << endl;
printUsage(cerr);
exit(1);
}
}
} while(next_option != -1);
}
#endif
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