/
pe.cpp
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/
pe.cpp
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#include "assert_helpers.h"
#include "pe.h"
using namespace std;
int PairedEndPolicy::peClassifyPair(
int64_t off1,
size_t len1, bool fw1, int64_t off2, size_t len2, bool fw2) const
{
assert_gt(len1, 0);
assert_gt(len2, 0);
size_t maxfrag = maxfrag_;
if (len1 > maxfrag && expandToFit_)
maxfrag = len1;
if (len2 > maxfrag && expandToFit_)
maxfrag = len2;
size_t minfrag = minfrag_;
if (minfrag < 1)
{
minfrag = 1;
}
bool oneLeft = false;
if (pol_ == PE_POLICY_FF)
{
if (fw1 != fw2)
{
return PE_ALS_DISCORD;
}
oneLeft = fw1;
}
else if (pol_ == PE_POLICY_RR)
{
if (fw1 != fw2)
{
return PE_ALS_DISCORD;
}
oneLeft = !fw1;
}
else if (pol_ == PE_POLICY_FR)
{
if (fw1 == fw2)
{
return PE_ALS_DISCORD;
}
oneLeft = fw1;
}
else if (pol_ == PE_POLICY_RF)
{
if (fw1 == fw2)
{
return PE_ALS_DISCORD;
}
oneLeft = !fw1;
}
int64_t fraglo = min<int64_t>(off1, off2);
int64_t fraghi = max<int64_t>(off1 + len1, off2 + len2);
assert_gt(fraghi, fraglo);
size_t frag = (size_t)(fraghi - fraglo);
if (frag > maxfrag || frag < minfrag)
{
return PE_ALS_DISCORD;
}
int64_t lo1 = off1;
int64_t hi1 = off1 + len1 - 1;
int64_t lo2 = off2;
int64_t hi2 = off2 + len2 - 1;
bool containment = false;
if ((lo1 >= lo2 && hi1 <= hi2) ||
(lo2 >= lo1 && hi2 <= hi1))
{
containment = true;
}
int type = PE_ALS_NORMAL;
bool olap = false;
if ((lo1 <= lo2 && hi1 >= lo2) ||
(lo1 <= hi2 && hi1 >= hi2) ||
containment)
{
olap = true;
if (!olapOk_)
return PE_ALS_DISCORD;
type = PE_ALS_OVERLAP;
}
if (!olap)
{
if ((oneLeft && lo2 < lo1) || (!oneLeft && lo1 < lo2))
{
return PE_ALS_DISCORD;
}
}
if (containment)
{
if (!containOk_)
return PE_ALS_DISCORD;
type = PE_ALS_CONTAIN;
}
if ((oneLeft && (hi1 > hi2 || lo2 < lo1)) ||
(!oneLeft && (hi2 > hi1 || lo1 < lo2)))
{
if (!dovetailOk_)
return PE_ALS_DISCORD;
type = PE_ALS_DOVETAIL;
}
return type;
}
bool PairedEndPolicy::otherMate(
bool is1,
bool fw, int64_t off, int64_t maxalcols, size_t reflen, size_t len1, size_t len2, bool &oleft, int64_t &oll, int64_t &olr, int64_t &orl, int64_t &orr, bool &ofw) const
{
assert_gt(len1, 0);
assert_gt(len2, 0);
assert_gt(maxfrag_, 0);
assert_geq(minfrag_, 0);
assert_geq(maxfrag_, minfrag_);
assert(maxalcols == -1 || maxalcols > 0);
pePolicyMateDir(pol_, is1, fw, oleft, ofw);
size_t alen = is1 ? len1 : len2;
size_t maxfrag = maxfrag_;
size_t minfrag = minfrag_;
if (minfrag < 1)
{
minfrag = 1;
}
if (len1 > maxfrag && expandToFit_)
maxfrag = len1;
if (len2 > maxfrag && expandToFit_)
maxfrag = len2;
if (!expandToFit_ && (len1 > maxfrag || len2 > maxfrag))
{
return false;
}
if (oleft)
{
oll = off + alen - maxfrag;
olr = off + alen - minfrag;
assert_geq(olr, oll);
orl = oll;
orr = off + maxfrag - 1;
assert_geq(olr, oll);
if (!olapOk_)
{
orr = min<int64_t>(orr, off - 1);
if (orr < olr)
olr = orr;
assert_leq(oll, olr);
assert_leq(orl, orr);
assert_geq(orr, olr);
}
else if (!dovetailOk_)
{
orr = min<int64_t>(orr, off + alen - 1);
assert_leq(oll, olr);
assert_leq(orl, orr);
}
else if (!flippingOk_ && maxalcols != -1)
{
orr = min<int64_t>(orr, off + alen - 1 + (maxalcols - 1));
assert_leq(oll, olr);
assert_leq(orl, orr);
}
assert_geq(olr, oll);
assert_geq(orr, orl);
assert_geq(orr, olr);
assert_geq(orl, oll);
}
else
{
orr = off + (maxfrag - 1);
orl = off + (minfrag - 1);
assert_geq(orr, orl);
oll = off + alen - maxfrag;
olr = orr;
assert_geq(olr, oll);
if (!olapOk_)
{
oll = max<int64_t>(oll, off + alen);
if (oll > orl)
orl = oll;
assert_leq(oll, olr);
assert_leq(orl, orr);
assert_geq(orl, oll);
}
else if (!dovetailOk_)
{
oll = max<int64_t>(oll, off);
assert_leq(oll, olr);
assert_leq(orl, orr);
}
else if (!flippingOk_ && maxalcols != -1)
{
oll = max<int64_t>(oll, off - maxalcols + 1);
assert_leq(oll, olr);
assert_leq(orl, orr);
}
assert_geq(olr, oll);
assert_geq(orr, orl);
assert_geq(orr, olr);
assert_geq(orl, oll);
}
return true;
}
#ifdef MAIN_PE
#include <string>
#include <sstream>
void testCaseClassify(
const string &name,
int pol,
size_t maxfrag,
size_t minfrag,
bool local,
bool flip,
bool dove,
bool cont,
bool olap,
bool expand,
int64_t off1,
size_t len1,
bool fw1,
int64_t off2,
size_t len2,
bool fw2,
int expect_class)
{
PairedEndPolicy pepol(
pol,
maxfrag,
minfrag,
local,
flip,
dove,
cont,
olap,
expand);
int ret = pepol.peClassifyPair(
off1,
len1, fw1, off2, len2, fw2);
assert_eq(expect_class, ret);
cout << "peClassifyPair: " << name << "...PASSED" << endl;
}
void testCaseOtherMate(
const string &name,
int pol,
size_t maxfrag,
size_t minfrag,
bool local,
bool flip,
bool dove,
bool cont,
bool olap,
bool expand,
bool is1,
bool fw,
int64_t off,
int64_t maxalcols,
size_t reflen,
size_t len1,
size_t len2,
bool expect_ret,
bool expect_oleft,
int64_t expect_oll,
int64_t expect_olr,
int64_t expect_orl,
int64_t expect_orr,
bool expect_ofw)
{
PairedEndPolicy pepol(
pol,
maxfrag,
minfrag,
local,
flip,
dove,
cont,
olap,
expand);
int64_t oll = 0, olr = 0;
int64_t orl = 0, orr = 0;
bool oleft = false, ofw = false;
bool ret = pepol.otherMate(
is1,
fw,
off,
maxalcols,
reflen,
len1,
len2,
oleft,
oll,
olr,
orl,
orr,
ofw);
assert(ret == expect_ret);
if (ret)
{
assert_eq(expect_oleft, oleft);
assert_eq(expect_oll, oll);
assert_eq(expect_olr, olr);
assert_eq(expect_orl, orl);
assert_eq(expect_orr, orr);
assert_eq(expect_ofw, ofw);
}
cout << "otherMate: " << name << "...PASSED" << endl;
}
int main(int argc, char **argv)
{
{
int policies[] = {PE_POLICY_FF, PE_POLICY_RR, PE_POLICY_FR, PE_POLICY_RF, PE_POLICY_FF, PE_POLICY_RR, PE_POLICY_FR, PE_POLICY_RF};
bool is1[] = {true, true, true, true, false, false, false, false};
bool fw[] = {true, false, true, false, false, true, true, false};
bool oleft[] = {false, false, false, false, false, false, false, false};
bool ofw[] = {true, false, false, true, false, true, false, true};
for (int i = 0; i < 8; i++)
{
ostringstream oss;
oss << "Simple";
oss << i;
testCaseOtherMate(
oss.str(),
policies[i],
30, 20, false, true, true, true, true, true, is1[i], fw[i], 100, -1, 200, 10, 10, true, oleft[i], 80, 129, 119, 129, ofw[i]);
}
}
{
int policies[] = {PE_POLICY_FF, PE_POLICY_RR, PE_POLICY_FR, PE_POLICY_RF, PE_POLICY_FF, PE_POLICY_RR, PE_POLICY_FR, PE_POLICY_RF};
bool is1[] = {false, false, false, false, true, true, true, true};
bool fw[] = {true, false, false, true, false, true, false, true};
bool oleft[] = {true, true, true, true, true, true, true, true};
bool ofw[] = {true, false, true, false, false, true, true, false};
for (int i = 0; i < 8; i++)
{
ostringstream oss;
oss << "Simple";
oss << (i + 8);
testCaseOtherMate(
oss.str(),
policies[i],
30, 20, false, true, true, true, true, true, is1[i], fw[i], 120, -1, 200, 10, 10, true, oleft[i], 100, 110, 100, 149, ofw[i]);
}
}
testCaseOtherMate(
"MinFragEqMax1",
PE_POLICY_FR,
30, 30, false, true, true, true, true, true, false, false, 120, -1, 200, 10, 10, true, true, 100, 100, 100, 149, true);
testCaseOtherMate(
"MinFragEqMax2",
PE_POLICY_FR,
30, 30, false, true, true, true, true, true, true, true, 100, -1, 200, 10, 10, true, false, 80, 129, 129, 129, false);
testCaseOtherMate(
"MinFragEqMax4NoDove1",
PE_POLICY_FR,
30, 25, false, true, false, true, true, true, true, true, 100, -1, 200, 10, 10, true, false, 100, 129, 124, 129, false);
testCaseOtherMate(
"MinFragEqMax4NoCont1",
PE_POLICY_FR,
30, 25, false, true, false, false, true, true, true, true, 100, -1, 200, 10, 10, true, false, 100, 129, 124, 129, false);
testCaseOtherMate(
"MinFragEqMax4NoOlap1",
PE_POLICY_FR,
30, 25, false, true, false, false, false, true, true, true, 100, -1, 200, 10, 10, true, false, 110, 129, 124, 129, false);
testCaseOtherMate(
"MinFragEqMax4NoDove2",
PE_POLICY_FR,
30, 25, false, true, false, true, true, true, false, false, 120, -1, 200, 10, 10, true, true, 100, 105, 100, 129, true);
testCaseOtherMate(
"MinFragEqMax4NoOlap2",
PE_POLICY_FR,
30, 25, false, true, false, false, false, true, false, false, 120, -1, 200, 10, 10, true, true, 100, 105, 100, 119, true);
{
int olls[] = {110};
int olrs[] = {299};
int orls[] = {149};
int orrs[] = {299};
for (int i = 0; i < 1; i++)
{
ostringstream oss;
oss << "Overhang1_";
oss << (i + 1);
testCaseOtherMate(
oss.str(),
PE_POLICY_FR,
200, 50, false, true, true, true, false, true, true, true, 100, -1, 200, 10, 10, true, false, olls[i], olrs[i], orls[i], orrs[i], false);
}
}
{
int olls[] = {-100};
int olrs[] = {50};
int orls[] = {-100};
int orrs[] = {89};
for (int i = 0; i < 1; i++)
{
ostringstream oss;
oss << "Overhang2_";
oss << (i + 1);
testCaseOtherMate(
oss.str(),
PE_POLICY_FR,
200, 50, false, true, true, true, false, true, true, false, 90, -1, 200, 10, 10, true, true, olls[i], olrs[i], orls[i], orrs[i], true);
}
}
{
int mate2offs[] = {150, 149, 149, 100, 99, 299, 1, 250, 250};
int mate2lens[] = {50, 50, 51, 100, 101, 1, 50, 50, 51};
int peExpects[] = {PE_ALS_NORMAL, PE_ALS_DISCORD, PE_ALS_OVERLAP, PE_ALS_CONTAIN, PE_ALS_DOVETAIL, PE_ALS_NORMAL, PE_ALS_DISCORD, PE_ALS_NORMAL, PE_ALS_DISCORD};
for (int i = 0; i < 9; i++)
{
ostringstream oss;
oss << "Simple1_";
oss << (i);
testCaseClassify(
oss.str(),
PE_POLICY_FR,
200, 100, false, true, true, true, true, true, 100, 50, true, mate2offs[i], mate2lens[i], false, peExpects[i]);
}
}
{
int mate1offs[] = {200, 201, 200, 200, 200, 100, 400, 100, 99};
int mate1lens[] = {50, 49, 51, 100, 101, 1, 50, 50, 51};
int peExpects[] = {PE_ALS_NORMAL, PE_ALS_DISCORD, PE_ALS_OVERLAP, PE_ALS_CONTAIN, PE_ALS_DOVETAIL, PE_ALS_NORMAL, PE_ALS_DISCORD, PE_ALS_NORMAL, PE_ALS_DISCORD};
for (int i = 0; i < 9; i++)
{
ostringstream oss;
oss << "Simple2_";
oss << (i);
testCaseClassify(
oss.str(),
PE_POLICY_FR,
200, 100, false, true, true, true, true, true, mate1offs[i], mate1lens[i], true, 250, 50, false, peExpects[i]);
}
}
testCaseOtherMate(
"Regression1",
PE_POLICY_FF,
50, 0, false, true, true, true, true, true, true, false, 3, -1, 53, 10, 10, true, true, -37, 13, -37, 52, false);
}
#endif