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Bugfix ihs freqs #59

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Bugfix ihs freqs #59

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fcb2168
fix to reporting DAF in ihs output
lauterbur Oct 23, 2019
7c2d177
fix to reporting DAF in ihs output
lauterbur Oct 23, 2019
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Binary file modified data/1000GP_Phase3.GBR.chr22.hap.gz
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Binary file modified data/chr22.map.gz
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4 changes: 3 additions & 1 deletion src/ihs.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -59,14 +59,16 @@ void calcIhsNoMpi(
std::cout << "Calculations took " << std::chrono::duration<double, std::milli>(diff).count() << "ms" << std::endl;

auto unStd = ihsfinder->unStdIHSByLine();
auto freQs = ihsfinder->freqsByLine();

std::ofstream out2(outfile);
out2 << "Index\tID\tFreq\tiHH_0\tiHH_1\tiHS\tStd iHS" << std::endl;

for (const auto& it : res)
{
auto s = unStd[it.first];
out2 << it.first << '\t' << hm.lineToId(it.first) << '\t' << s.freq << '\t' << s.iHH_0 << '\t' << s.iHH_1 << '\t' << s.iHS << "\t" << it.second << std::endl;
auto q = freQs[it.first];
out2 << it.first << '\t' << hm.lineToId(it.first) << '\t' << q << '\t' << s.iHH_0 << '\t' << s.iHH_1 << '\t' << s.iHS << "\t" << it.second << std::endl;
}
std::cout << "# valid loci: " << res.size() << std::endl;
std::cout << "# loci with MAF <= " << minMAF << ": " << ihsfinder->numOutsideMaf() << std::endl;
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4 changes: 3 additions & 1 deletion src/ihs_mpi.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -152,6 +152,7 @@ void calcIhsMpi(
IHSFinder::LineMap res = ihsfinder->normalize();

auto unStd = ihsfinder->unStdIHSByLine();
auto freQs = ihsfinder->freqsByLine();

/*std::ofstream out(outfile);
out << "Location\tiHH_0\tiHH_1\tiHS" << std::endl;
Expand All @@ -165,7 +166,8 @@ void calcIhsMpi(
for (const auto& it : res)
{
auto s = unStd[it.first];
out2 << it.first << '\t' << hap.lineToId(it.first) << '\t' << s.freq << '\t' << s.iHH_0 << '\t' << s.iHH_1 << '\t' << s.iHS << "\t" << it.second << std::endl;
auto q = freQs[it.first];
out2 << it.first << '\t' << hap.lineToId(it.first) << '\t' << q << '\t' << s.iHH_0 << '\t' << s.iHH_1 << '\t' << s.iHS << "\t" << it.second << std::endl;
}
std::cout << "# valid loci: " << res.size() << std::endl;
std::cout << "# loci with MAF <= " << minMAF << ": " << ihsfinder->numOutsideMaf() << std::endl;
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