add knucleotide example

2026-08-30 00:50:38 +08:00 · 2019-04-07 20:49:06 -04:00
parent e046f6c531
commit 5654f72bdd
4 changed files with 4575 additions and 1 deletions
@@ -116,6 +116,6 @@ if (PHMAP_BUILD_EXAMPLES)
    add_executable(ex_hash_std examples/hash_std.cc)
    add_executable(ex_two_files examples/f1.cc examples/f2.cc)
    add_executable(ex_insert_bench examples/insert_bench.cc)
-    ##add_executable(ex_knucleotide examples/knucleotide.cc)
+    add_executable(ex_knucleotide examples/knucleotide.cc)
 endif()

@@ -0,0 +1,171 @@
+>ONE Homo sapiens alu
+GGCCGGGCGCGGTGGCTCACGCCTGTAATCCCAGCACTTTGGGAGGCCGAGGCGGGCGGA
+TCACCTGAGGTCAGGAGTTCGAGACCAGCCTGGCCAACATGGTGAAACCCCGTCTCTACT
+AAAAATACAAAAATTAGCCGGGCGTGGTGGCGCGCGCCTGTAATCCCAGCTACTCGGGAG
+GCTGAGGCAGGAGAATCGCTTGAACCCGGGAGGCGGAGGTTGCAGTGAGCCGAGATCGCG
+CCACTGCACTCCAGCCTGGGCGACAGAGCGAGACTCCGTCTCAAAAAGGCCGGGCGCGGT
+GGCTCACGCCTGTAATCCCAGCACTTTGGGAGGCCGAGGCGGGCGGATCACCTGAGGTCA
+GGAGTTCGAGACCAGCCTGGCCAACATGGTGAAACCCCGTCTCTACTAAAAATACAAAAA
+TTAGCCGGGCGTGGTGGCGCGCGCCTGTAATCCCAGCTACTCGGGAGGCTGAGGCAGGAG
+AATCGCTTGAACCCGGGAGGCGGAGGTTGCAGTGAGCCGAGATCGCGCCACTGCACTCCA
+GCCTGGGCGACAGAGCGAGACTCCGTCTCAAAAAGGCCGGGCGCGGTGGCTCACGCCTGT
+AATCCCAGCACTTTGGGAGGCCGAGGCGGGCGGATCACCTGAGGTCAGGAGTTCGAGACC
+AGCCTGGCCAACATGGTGAAACCCCGTCTCTACTAAAAATACAAAAATTAGCCGGGCGTG
+GTGGCGCGCGCCTGTAATCCCAGCTACTCGGGAGGCTGAGGCAGGAGAATCGCTTGAACC
+CGGGAGGCGGAGGTTGCAGTGAGCCGAGATCGCGCCACTGCACTCCAGCCTGGGCGACAG
+AGCGAGACTCCGTCTCAAAAAGGCCGGGCGCGGTGGCTCACGCCTGTAATCCCAGCACTT
+TGGGAGGCCGAGGCGGGCGGATCACCTGAGGTCAGGAGTTCGAGACCAGCCTGGCCAACA
+TGGTGAAACCCCGTCTCTACTAAAAATACAAAAATTAGCCGGGCGTGGTGGCGCGCGCCT
+GTAATCCCAGCTACTCGGGAGGCTGAGGCAGGAGAATCGCTTGAACCCGGGAGGCGGAGG
+TTGCAGTGAGCCGAGATCGCGCCACTGCACTCCAGCCTGGGCGACAGAGCGAGACTCCGT
+CTCAAAAAGGCCGGGCGCGGTGGCTCACGCCTGTAATCCCAGCACTTTGGGAGGCCGAGG
+CGGGCGGATCACCTGAGGTCAGGAGTTCGAGACCAGCCTGGCCAACATGGTGAAACCCCG
+TCTCTACTAAAAATACAAAAATTAGCCGGGCGTGGTGGCGCGCGCCTGTAATCCCAGCTA
+CTCGGGAGGCTGAGGCAGGAGAATCGCTTGAACCCGGGAGGCGGAGGTTGCAGTGAGCCG
+AGATCGCGCCACTGCACTCCAGCCTGGGCGACAGAGCGAGACTCCGTCTCAAAAAGGCCG
+GGCGCGGTGGCTCACGCCTGTAATCCCAGCACTTTGGGAGGCCGAGGCGGGCGGATCACC
+TGAGGTCAGGAGTTCGAGACCAGCCTGGCCAACATGGTGAAACCCCGTCTCTACTAAAAA
+TACAAAAATTAGCCGGGCGTGGTGGCGCGCGCCTGTAATCCCAGCTACTCGGGAGGCTGA
+GGCAGGAGAATCGCTTGAACCCGGGAGGCGGAGGTTGCAGTGAGCCGAGATCGCGCCACT
+GCACTCCAGCCTGGGCGACAGAGCGAGACTCCGTCTCAAAAAGGCCGGGCGCGGTGGCTC
+ACGCCTGTAATCCCAGCACTTTGGGAGGCCGAGGCGGGCGGATCACCTGAGGTCAGGAGT
+TCGAGACCAGCCTGGCCAACATGGTGAAACCCCGTCTCTACTAAAAATACAAAAATTAGC
+CGGGCGTGGTGGCGCGCGCCTGTAATCCCAGCTACTCGGGAGGCTGAGGCAGGAGAATCG
+CTTGAACCCGGGAGGCGGAGGTTGCAGTGAGCCGAGATCGCGCCACTGCACTCCAGCCTG
+GGCGACAGAGCGAGACTCCG
+>TWO IUB ambiguity codes
+cttBtatcatatgctaKggNcataaaSatgtaaaDcDRtBggDtctttataattcBgtcg
+tactDtDagcctatttSVHtHttKtgtHMaSattgWaHKHttttagacatWatgtRgaaa
+NtactMcSMtYtcMgRtacttctWBacgaaatatagScDtttgaagacacatagtVgYgt
+cattHWtMMWcStgttaggKtSgaYaaccWStcgBttgcgaMttBYatcWtgacaYcaga
+gtaBDtRacttttcWatMttDBcatWtatcttactaBgaYtcttgttttttttYaaScYa
+HgtgttNtSatcMtcVaaaStccRcctDaataataStcYtRDSaMtDttgttSagtRRca
+tttHatSttMtWgtcgtatSSagactYaaattcaMtWatttaSgYttaRgKaRtccactt
+tattRggaMcDaWaWagttttgacatgttctacaaaRaatataataaMttcgDacgaSSt
+acaStYRctVaNMtMgtaggcKatcttttattaaaaagVWaHKYagtttttatttaacct
+tacgtVtcVaattVMBcttaMtttaStgacttagattWWacVtgWYagWVRctDattBYt
+gtttaagaagattattgacVatMaacattVctgtBSgaVtgWWggaKHaatKWcBScSWa
+accRVacacaaactaccScattRatatKVtactatatttHttaagtttSKtRtacaaagt
+RDttcaaaaWgcacatWaDgtDKacgaacaattacaRNWaatHtttStgttattaaMtgt
+tgDcgtMgcatBtgcttcgcgaDWgagctgcgaggggVtaaScNatttacttaatgacag
+cccccacatYScaMgtaggtYaNgttctgaMaacNaMRaacaaacaKctacatagYWctg
+ttWaaataaaataRattagHacacaagcgKatacBttRttaagtatttccgatctHSaat
+actcNttMaagtattMtgRtgaMgcataatHcMtaBSaRattagttgatHtMttaaKagg
+YtaaBataSaVatactWtataVWgKgttaaaacagtgcgRatatacatVtHRtVYataSa
+KtWaStVcNKHKttactatccctcatgWHatWaRcttactaggatctataDtDHBttata
+aaaHgtacVtagaYttYaKcctattcttcttaataNDaaggaaaDYgcggctaaWSctBa
+aNtgctggMBaKctaMVKagBaactaWaDaMaccYVtNtaHtVWtKgRtcaaNtYaNacg
+gtttNattgVtttctgtBaWgtaattcaagtcaVWtactNggattctttaYtaaagccgc
+tcttagHVggaYtgtNcDaVagctctctKgacgtatagYcctRYHDtgBattDaaDgccK
+tcHaaStttMcctagtattgcRgWBaVatHaaaataYtgtttagMDMRtaataaggatMt
+ttctWgtNtgtgaaaaMaatatRtttMtDgHHtgtcattttcWattRSHcVagaagtacg
+ggtaKVattKYagactNaatgtttgKMMgYNtcccgSKttctaStatatNVataYHgtNa
+BKRgNacaactgatttcctttaNcgatttctctataScaHtataRagtcRVttacDSDtt
+aRtSatacHgtSKacYagttMHtWataggatgactNtatSaNctataVtttRNKtgRacc
+tttYtatgttactttttcctttaaacatacaHactMacacggtWataMtBVacRaSaatc
+cgtaBVttccagccBcttaRKtgtgcctttttRtgtcagcRttKtaaacKtaaatctcac
+aattgcaNtSBaaccgggttattaaBcKatDagttactcttcattVtttHaaggctKKga
+tacatcBggScagtVcacattttgaHaDSgHatRMaHWggtatatRgccDttcgtatcga
+aacaHtaagttaRatgaVacttagattVKtaaYttaaatcaNatccRttRRaMScNaaaD
+gttVHWgtcHaaHgacVaWtgttScactaagSgttatcttagggDtaccagWattWtRtg
+ttHWHacgattBtgVcaYatcggttgagKcWtKKcaVtgaYgWctgYggVctgtHgaNcV
+taBtWaaYatcDRaaRtSctgaHaYRttagatMatgcatttNattaDttaattgttctaa
+ccctcccctagaWBtttHtBccttagaVaatMcBHagaVcWcagBVttcBtaYMccagat
+gaaaaHctctaacgttagNWRtcggattNatcRaNHttcagtKttttgWatWttcSaNgg
+gaWtactKKMaacatKatacNattgctWtatctaVgagctatgtRaHtYcWcttagccaa
+tYttWttaWSSttaHcaaaaagVacVgtaVaRMgattaVcDactttcHHggHRtgNcctt
+tYatcatKgctcctctatVcaaaaKaaaagtatatctgMtWtaaaacaStttMtcgactt
+taSatcgDataaactaaacaagtaaVctaggaSccaatMVtaaSKNVattttgHccatca
+cBVctgcaVatVttRtactgtVcaattHgtaaattaaattttYtatattaaRSgYtgBag
+aHSBDgtagcacRHtYcBgtcacttacactaYcgctWtattgSHtSatcataaatataHt
+cgtYaaMNgBaatttaRgaMaatatttBtttaaaHHKaatctgatWatYaacttMctctt
+ttVctagctDaaagtaVaKaKRtaacBgtatccaaccactHHaagaagaaggaNaaatBW
+attccgStaMSaMatBttgcatgRSacgttVVtaaDMtcSgVatWcaSatcttttVatag
+ttactttacgatcaccNtaDVgSRcgVcgtgaacgaNtaNatatagtHtMgtHcMtagaa
+attBgtataRaaaacaYKgtRccYtatgaagtaataKgtaaMttgaaRVatgcagaKStc
+tHNaaatctBBtcttaYaBWHgtVtgacagcaRcataWctcaBcYacYgatDgtDHccta
+>THREE Homo sapiens frequency
+aacacttcaccaggtatcgtgaaggctcaagattacccagagaacctttgcaatataaga
+atatgtatgcagcattaccctaagtaattatattctttttctgactcaaagtgacaagcc
+ctagtgtatattaaatcggtatatttgggaaattcctcaaactatcctaatcaggtagcc
+atgaaagtgatcaaaaaagttcgtacttataccatacatgaattctggccaagtaaaaaa
+tagattgcgcaaaattcgtaccttaagtctctcgccaagatattaggatcctattactca
+tatcgtgtttttctttattgccgccatccccggagtatctcacccatccttctcttaaag
+gcctaatattacctatgcaaataaacatatattgttgaaaattgagaacctgatcgtgat
+tcttatgtgtaccatatgtatagtaatcacgcgactatatagtgctttagtatcgcccgt
+gggtgagtgaatattctgggctagcgtgagatagtttcttgtcctaatatttttcagatc
+gaatagcttctatttttgtgtttattgacatatgtcgaaactccttactcagtgaaagtc
+atgaccagatccacgaacaatcttcggaatcagtctcgttttacggcggaatcttgagtc
+taacttatatcccgtcgcttactttctaacaccccttatgtatttttaaaattacgttta
+ttcgaacgtacttggcggaagcgttattttttgaagtaagttacattgggcagactcttg
+acattttcgatacgactttctttcatccatcacaggactcgttcgtattgatatcagaag
+ctcgtgatgattagttgtcttctttaccaatactttgaggcctattctgcgaaatttttg
+ttgccctgcgaacttcacataccaaggaacacctcgcaacatgccttcatatccatcgtt
+cattgtaattcttacacaatgaatcctaagtaattacatccctgcgtaaaagatggtagg
+ggcactgaggatatattaccaagcatttagttatgagtaatcagcaatgtttcttgtatt
+aagttctctaaaatagttacatcgtaatgttatctcgggttccgcgaataaacgagatag
+attcattatatatggccctaagcaaaaacctcctcgtattctgttggtaattagaatcac
+acaatacgggttgagatattaattatttgtagtacgaagagatataaaaagatgaacaat
+tactcaagtcaagatgtatacgggatttataataaaaatcgggtagagatctgctttgca
+attcagacgtgccactaaatcgtaatatgtcgcgttacatcagaaagggtaactattatt
+aattaataaagggcttaatcactacatattagatcttatccgatagtcttatctattcgt
+tgtatttttaagcggttctaattcagtcattatatcagtgctccgagttctttattattg
+ttttaaggatgacaaaatgcctcttgttataacgctgggagaagcagactaagagtcgga
+gcagttggtagaatgaggctgcaaaagacggtctcgacgaatggacagactttactaaac
+caatgaaagacagaagtagagcaaagtctgaagtggtatcagcttaattatgacaaccct
+taatacttccctttcgccgaatactggcgtggaaaggttttaaaagtcgaagtagttaga
+ggcatctctcgctcataaataggtagactactcgcaatccaatgtgactatgtaatactg
+ggaacatcagtccgcgatgcagcgtgtttatcaaccgtccccactcgcctggggagacat
+gagaccacccccgtggggattattagtccgcagtaatcgactcttgacaatccttttcga
+ttatgtcatagcaatttacgacagttcagcgaagtgactactcggcgaaatggtattact
+aaagcattcgaacccacatgaatgtgattcttggcaatttctaatccactaaagcttttc
+cgttgaatctggttgtagatatttatataagttcactaattaagatcacggtagtatatt
+gatagtgatgtctttgcaagaggttggccgaggaatttacggattctctattgatacaat
+ttgtctggcttataactcttaaggctgaaccaggcgtttttagacgacttgatcagctgt
+tagaatggtttggactccctctttcatgtcagtaacatttcagccgttattgttacgata
+tgcttgaacaatattgatctaccacacacccatagtatattttataggtcatgctgttac
+ctacgagcatggtattccacttcccattcaatgagtattcaacatcactagcctcagaga
+tgatgacccacctctaataacgtcacgttgcggccatgtgaaacctgaacttgagtagac
+gatatcaagcgctttaaattgcatataacatttgagggtaaagctaagcggatgctttat
+ataatcaatactcaataataagatttgattgcattttagagttatgacacgacatagttc
+actaacgagttactattcccagatctagactgaagtactgatcgagacgatccttacgtc
+gatgatcgttagttatcgacttaggtcgggtctctagcggtattggtacttaaccggaca
+ctatactaataacccatgatcaaagcataacagaatacagacgataatttcgccaacata
+tatgtacagaccccaagcatgagaagctcattgaaagctatcattgaagtcccgctcaca
+atgtgtcttttccagacggtttaactggttcccgggagtcctggagtttcgacttacata
+aatggaaacaatgtattttgctaatttatctatagcgtcatttggaccaatacagaatat
+tatgttgcctagtaatccactataacccgcaagtgctgatagaaaatttttagacgattt
+ataaatgccccaagtatccctcccgtgaatcctccgttatactaattagtattcgttcat
+acgtataccgcgcatatatgaacatttggcgataaggcgcgtgaattgttacgtgacaga
+gatagcagtttcttgtgatatggttaacagacgtacatgaagggaaactttatatctata
+gtgatgcttccgtagaaataccgccactggtctgccaatgatgaagtatgtagctttagg
+tttgtactatgaggctttcgtttgtttgcagagtataacagttgcgagtgaaaaaccgac
+gaatttatactaatacgctttcactattggctacaaaatagggaagagtttcaatcatga
+gagggagtatatggatgctttgtagctaaaggtagaacgtatgtatatgctgccgttcat
+tcttgaaagatacataagcgataagttacgacaattataagcaacatccctaccttcgta
+acgatttcactgttactgcgcttgaaatacactatggggctattggcggagagaagcaga
+tcgcgccgagcatatacgagacctataatgttgatgatagagaaggcgtctgaattgata
+catcgaagtacactttctttcgtagtatctctcgtcctctttctatctccggacacaaga
+attaagttatatatatagagtcttaccaatcatgttgaatcctgattctcagagttcttt
+ggcgggccttgtgatgactgagaaacaatgcaatattgctccaaatttcctaagcaaatt
+ctcggttatgttatgttatcagcaaagcgttacgttatgttatttaaatctggaatgacg
+gagcgaagttcttatgtcggtgtgggaataattcttttgaagacagcactccttaaataa
+tatcgctccgtgtttgtatttatcgaatgggtctgtaaccttgcacaagcaaatcggtgg
+tgtatatatcggataacaattaatacgatgttcatagtgacagtatactgatcgagtcct
+ctaaagtcaattacctcacttaacaatctcattgatgttgtgtcattcccggtatcgccc
+gtagtatgtgctctgattgaccgagtgtgaaccaaggaacatctactaatgcctttgtta
+ggtaagatctctctgaattccttcgtgccaacttaaaacattatcaaaatttcttctact
+tggattaactacttttacgagcatggcaaattcccctgtggaagacggttcattattatc
+ggaaaccttatagaaattgcgtgttgactgaaattagatttttattgtaagagttgcatc
+tttgcgattcctctggtctagcttccaatgaacagtcctcccttctattcgacatcgggt
+ccttcgtacatgtctttgcgatgtaataattaggttcggagtgtggccttaatgggtgca
+actaggaatacaacgcaaatttgctgacatgatagcaaatcggtatgccggcaccaaaac
+gtgctccttgcttagcttgtgaatgagactcagtagttaaataaatccatatctgcaatc
+gattccacaggtattgtccactatctttgaactactctaagagatacaagcttagctgag
+accgaggtgtatatgactacgctgatatctgtaaggtaccaatgcaggcaaagtatgcga
+gaagctaataccggctgtttccagctttataagattaaaatttggctgtcctggcggcct
+cagaattgttctatcgtaatcagttggttcattaattagctaagtacgaggtacaactta
+tctgtcccagaacagctccacaagtttttttacagccgaaacccctgtgtgaatcttaat
+atccaagcgcgttatctgattagagtttacaactcagtattttatcagtacgttttgttt
+ccaacattacccggtatgacaaaatgacgccacgtgtcgaataatggtctgaccaatgta
+ggaagtgaaaagataaatat
@@ -0,0 +1,232 @@
+// ------------------------------------------------------------------
+// run with: knucleotide 0 < ../examples/knucleotide-input.txt
+// ------------------------------------------------------------------
+//
+// output should be:
+// 
+// T 31.520
+// A 29.600
+// C 19.480
+// G 19.400
+// 
+// AT 9.922
+// TT 9.602
+// TA 9.402
+// AA 8.402
+// GA 6.321
+// TC 6.301
+// TG 6.201
+// GT 6.041
+// CT 5.961
+// AG 5.841
+// CA 5.461
+// AC 5.441
+// CC 4.041
+// CG 4.021
+// GC 3.701
+// GG 3.341
+// 
+// 54	GGT
+// 24	GGTA
+// 4	GGTATT
+// 0	GGTATTTTAATT
+// 0	GGTATTTTAATTTATAGT
+// ------------------------------------------------------------------
+#include <iostream>
+#include <iomanip>
+#include <cstdint>
+#include <string>
+#include <algorithm>
+#include <map>
+#include <thread>
+#include <type_traits>
+#include <cstring>
+#include <array>
+#include <vector>
+#include <cassert>
+#include <unordered_map>
+
+// ------------------------------------------------------------------
+struct Cfg {
+    static constexpr size_t thread_count = 4;
+    static constexpr unsigned to_char[4] = {'A', 'C', 'T', 'G'};
+    unsigned char to_num[128];
+    using Data = std::vector<unsigned char>;
+
+    Cfg() {
+        to_num['A'] = to_num['a'] = 0;
+        to_num['C'] = to_num['c'] = 1;
+        to_num['T'] = to_num['t'] = 2;
+        to_num['G'] = to_num['g'] = 3;
+    }
+} const cfg;
+
+// ------------------------------------------------------------------
+template <size_t size>
+struct Key
+{
+    // select type to use for 'data', if hash key can fit on 32-bit integer
+    // then use uint32_t else use uint64_t.
+    using Data = typename std::conditional<size<=16, uint32_t, uint64_t>::type;
+
+    struct Hash {
+        Data operator()(const Key& t)const{ return t._data; }
+    };
+
+    Key() : _data(0) {
+    }
+
+    Key(const char *str) {
+        _data = 0;
+        for(unsigned i = 0; i < size; ++i){
+            _data <<= 2;
+            _data |= cfg.to_num[unsigned(str[i])];
+        }
+    }
+
+    // initialize hash from input data
+    void InitKey(const unsigned char *data) {
+        for(unsigned i = 0; i < size; ++i){
+            _data <<= 2;
+            _data |= data[i];
+        }
+    }
+
+    // updates the key with 1 byte
+    void UpdateKey(const unsigned char data) {
+        _data <<= 2;
+        _data |= data;
+    }
+
+    // masks out excess information
+    void MaskKey() {
+        _data &= _mask;
+    }
+
+    // implicit casting operator to string
+    operator std::string() const {
+        std::string tmp;
+        Data data = _data;
+        for(size_t i = 0; i != size; ++i, data >>= 2)
+            tmp += cfg.to_char[data & 3ull];
+        std::reverse(tmp.begin(), tmp.end());
+        return std::move(tmp);
+    }
+
+    bool operator== (const Key& in) const {
+        return _data == in._data;
+    }
+private:
+    static constexpr Data _mask = ~(Data(-1) << (2 * size));
+    Data _data;
+};
+
+// ------------------------------------------------------------------
+template <size_t size, typename K = Key<size> >
+using HashTable = std::unordered_map<K, unsigned, typename K::Hash>;
+
+// ------------------------------------------------------------------
+template <size_t size>
+void Calculate(const Cfg::Data& input, size_t begin, HashTable<size>& table)
+{
+    // original implementation fully recomputes the hash key for each
+    // insert to the hash table. This implementation only partially
+    // updates the hash, this is the same with C GCC, Rust #6 and Rust #4
+    Key<size> key;
+    // initialize key
+    key.InitKey(input.data() + begin);
+    // use key to increment value
+    ++table[key];
+
+    auto itr_begin = input.data() + begin + cfg.thread_count;
+    auto itr_end = (input.data() + input.size() + 1) - size;
+    for(;itr_begin < itr_end; itr_begin += cfg.thread_count) {
+        // update the key 1 byte at a time
+        constexpr size_t nsize = std::min(size, cfg.thread_count);
+        for(unsigned i = 0; i < nsize; ++i)
+            key.UpdateKey( itr_begin[i] );
+
+        // then finally mask out excess information
+        key.MaskKey();
+
+        // then use key to increment value
+        ++table[key];
+    }
+}
+
+// ------------------------------------------------------------------
+template <size_t size>
+auto CalculateInThreads(const Cfg::Data& input)
+{
+    HashTable<size> hash_tables[cfg.thread_count];
+    std::thread threads[cfg.thread_count];
+
+    auto invoke = [&](unsigned begin) {
+        Calculate<size>(input, begin, hash_tables[begin]);
+    };
+
+    for(unsigned i = 0; i < cfg.thread_count; ++i)
+        threads[i] = std::thread(invoke, i);
+
+    for(auto& i : threads)
+        i.join();
+
+    auto& frequencies = hash_tables[0];
+    for(unsigned i = 1 ; i < cfg.thread_count; ++i)
+        for(auto& j : hash_tables[i])
+            frequencies[j.first] += j.second;
+    // return the 'frequency' by move instead of copy.
+    return std::move(frequencies);
+}
+
+// ------------------------------------------------------------------
+template <unsigned size>
+void WriteFrequencies(const Cfg::Data& input)
+{
+    // we "receive" the returned object by move instead of copy.
+    auto&& frequencies = CalculateInThreads<size>(input);
+    std::map<unsigned, std::string, std::greater<unsigned>> freq;
+    for(const auto& i: frequencies)
+        freq.insert({i.second, i.first});
+
+    const unsigned sum = input.size() + 1 - size;
+    for(const auto& i : freq)
+        std::cout << i.second << ' ' << (sum ? double(100 * i.first) / sum : 0.0) << '\n';
+    std::cout << '\n';
+}
+
+// ------------------------------------------------------------------
+template <unsigned size>
+void WriteCount( const Cfg::Data& input, const char *text ) {
+    // we "receive" the returned object by move instead of copy.
+    auto&& frequencies = CalculateInThreads<size>(input);
+    std::cout << frequencies[Key<size>(text)] << '\t' << text << '\n';
+}
+
+// ------------------------------------------------------------------
+int main()
+{
+    Cfg::Data data;
+    std::array<char, 256> buf;
+
+    while(fgets(buf.data(), buf.size(), stdin) && memcmp(">THREE", buf.data(), 6));
+    while(fgets(buf.data(), buf.size(), stdin) && buf.front() != '>') {
+        if(buf.front() != ';'){
+            auto i = std::find(buf.begin(), buf.end(), '\n');
+            data.insert(data.end(), buf.begin(), i);
+        }
+    }
+    std::transform(data.begin(), data.end(), data.begin(), [](auto c){
+        return cfg.to_num[c];
+    });
+    std::cout << std::setprecision(3) << std::setiosflags(std::ios::fixed);
+
+    WriteFrequencies<1>(data);
+    WriteFrequencies<2>(data);
+    // value at left is the length of the passed string.
+    WriteCount<3>(data, "GGT");
+    WriteCount<4>(data, "GGTA");
+    WriteCount<6>(data, "GGTATT");
+    WriteCount<12>(data, "GGTATTTTAATT");
+    WriteCount<18>(data, "GGTATTTTAATTTATAGT");
+}