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#include <cstdlib>
#include <iostream>
#include <fstream>
#include <string>
#include <gtest/gtest.h>
#include <boost/graph/adjacency_list.hpp>
#include "Alignment.hpp"
using namespace dagcon;
std::string dataDir() {
char const* val = getenv("PBDAGCON_TEST_DATA_DIR");
if (!val || !*val) {
return ".";
}
return val;
}
TEST(Alignment, Normalize) {
Alignment a, b;
a.start = 1;
// test mismatch
b.qstr = "CAC";
b.tstr = "CGC";
b = normalizeGaps(b);
EXPECT_EQ("C-AC", b.qstr);
EXPECT_EQ("CG-C", b.tstr);
// test shifting gaps on read
b.qstr = "-C--CGT";
b.tstr = "CCGAC-T";
b = normalizeGaps(b);
EXPECT_EQ("CCG--T", b.qstr);
EXPECT_EQ("CCGACT", b.tstr);
// another gap reference push
a.tstr = "ATATTA---GGC";
a.qstr = "ATAT-AGCCGGC";
b = a;
b = normalizeGaps(b);
// query remains unchanged
EXPECT_EQ(a.qstr, b.qstr);
// target shifts the G bases to the left
EXPECT_EQ("ATATTAG--G-C", b.tstr);
}
TEST(Alignment, ParseBasic) {
std::string fn = dataDir() + "basic.m5";
std::ifstream file(fn.c_str());
ASSERT_TRUE(file.good());
Alignment aln;
file >> aln;
EXPECT_EQ(1, aln.start);
EXPECT_EQ("CAC", aln.qstr);
EXPECT_EQ("CGC", aln.tstr);
file >> aln;
EXPECT_EQ(1, aln.start);
EXPECT_EQ("AATTGGCC", aln.qstr);
EXPECT_EQ("GGCCAATT", aln.tstr);
}
TEST(Alignment, ParseQuery) {
std::string fn = dataDir() + "parsequery.m5";
std::ifstream file(fn.c_str());
ASSERT_TRUE(file.good());
Alignment aln;
Alignment::groupByTarget = false;
file >> aln;
EXPECT_EQ("m130110_062238_00114_c100480560100000001823075906281381_s1_p0/311/1102_3151",
aln.id);
EXPECT_EQ(2049, aln.tlen);
EXPECT_EQ(8, aln.start);
EXPECT_EQ("CTGCATGCT", aln.tstr.substr(0,9));
EXPECT_EQ("CTGCA--CT", aln.qstr.substr(0,9));
}
TEST(Alignment, Trim) {
std::string const t = "ACG-TCA-GCA";
std::string const q = "AC-C-C-T---";
{
dagcon::Alignment aln;
aln.tstr = t;
aln.qstr = q;
aln.start = 1;
aln.strand = '-';
trimAln(aln, 0);
EXPECT_EQ(1, aln.start);
EXPECT_EQ(t, aln.tstr);
EXPECT_EQ(q, aln.qstr);
}
{
dagcon::Alignment aln;
aln.tstr = t;
aln.qstr = q;
aln.start = 1;
aln.strand = '-';
trimAln(aln, 3);
EXPECT_EQ(4, aln.start);
EXPECT_EQ("-TCA-", aln.tstr);
EXPECT_EQ("C-C-T", aln.qstr);
}
{
dagcon::Alignment aln;
aln.tstr = t;
aln.qstr = q;
aln.start = 1;
aln.strand = '-';
trimAln(aln, 4);
EXPECT_EQ(5, aln.start);
EXPECT_EQ("C", aln.tstr);
EXPECT_EQ("C", aln.qstr);
}
{
dagcon::Alignment aln;
aln.tstr = t;
aln.qstr = q;
aln.start = 1;
aln.strand = '-';
trimAln(aln, 5);
EXPECT_EQ(6, aln.start);
EXPECT_EQ("", aln.tstr);
EXPECT_EQ("", aln.qstr);
}
{
dagcon::Alignment aln;
aln.tstr = t;
aln.qstr = q;
aln.start = 1;
aln.strand = '-';
trimAln(aln, 500);
// EXPECT_EQ(1 + 9, aln.start); // start could be anything, really
EXPECT_EQ("", aln.tstr);
EXPECT_EQ("", aln.qstr);
}
}
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