slayer.cpp

   1 /*
   2  *  slayer.cpp
   3  *  Mothur
   4  *
   5  *  Created by westcott on 9/25/09.
   6  *  Copyright 2009 Schloss Lab. All rights reserved.
   7  *
   8  */
   9
  10 #include "slayer.h"
  11
  12 /***********************************************************************/
  13 Slayer::Slayer(int win, int increment, int parentThreshold, float div, int i, int snp, int mi) :
  14                 minBS(mi), windowSize(win), windowStep(increment), parentFragmentThreshold(parentThreshold), divRThreshold(div), iters(i), percentSNPSample(snp){ m = MothurOut::getInstance(); }
  15 /***********************************************************************/
  16 string Slayer::getResults(Sequence* query, vector<Sequence*> refSeqs) {
  17         try {
  18                 vector<data_struct> all; all.clear();
  19                 myQuery = *query;
  20                 /*cout << "here" << endl;
  21                 query->setName("S000381746"); query->setAligned("...............................................................................................................................................A-C-GC--TGG-C--G-GC-A-GG--C----C-T--AACACA-T-GC-A-AGT-CGA-G-CG----------G-CAG-CG-G---------------------------GA-GG-A-AG----------------------------------------------------CTT-G----------------------------------------------------------------------------------CTT-CCTC----------------G-CC--G--GC--G--AG-C-GG-C-GG-A--C-------------GGG-TGAGT-A--AT-GT-C-T-G-GG---G-A--T-CT-G--C-C-CGA--TG-G------------------------------------------------------------------A-GG----GGG-AT-AA-CCA-------------------------C-T-G-----------------------GAA-A---CGG-TGG-CTAA-TA---CC-G--C-AT-A----------A--------------------C-------------------------------------GT-C-----------------------------------------------------------------------------------------------------------------------G-CA-A--------------------------------------------------------------------------------------------------------------------------------------G-A-C---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CAAA--G-T-G-GG-----G--GA-C--C--------------------------------------------------------------------------------------------------------------------TTC-G----------------------------------------------------------------------------------------------------------------------G-G--CC-TC--A---C-A--------------C----C-A---T-CG-G---AT---G-A-----A-CCC-AGA--T-GGG--A------TT--A--G-CT-A----G---TAGG-T-G-GG-G-T----AAT-GG-C-T-C-ACCT--A-GG-C-G--A-CG-A------------TCC-C-T------AG-CT-G-G-TCT-G-AG----A--GG-AT--G-AC-C-AG-CCAC-A-CTGGA--A-C-TG-A-GA-C-AC-G-G-TCCAGA-CTCC-TAC-G--G-G-A-G-GC-A-GC-A-G-TG---GG-G-A-ATA-TTGCA-C-AA-T-GG--GC-GC-A----A-G-CC-T-GA-TG-CA-GCCA-TGCC-G-CG-T---G-T-G--T--GA-A-G--A--A-G-G-CC-----TT-CG---------G-G-T-T-G-T--A---AA-G-CAC--------TT-TC-A-G--C-GAG----GA-G--G---AA-GGTG---GTGA-GC----T--T--AA-T---A----------CG-CTCAT-CAA-TT-GA-CG-TT-A-C-TC-G-CA-G---------AA-----------GAAGC-ACC-GG-C-TAA---C--T-CCGT--GCCA--G-C---A--GCCG---C-GG--TA-AT--AC---GG-AG-GGT-GCA-A-G-CG-TTAA-T-CGG-AA-TT-A--C-T--GGGC-GTA----AA-GCGC-AC--G-CA-G-G-C-G------------G--T-TT-G-T-T-AA----G-T-C-A---G-ATG-TG-A-AA-TC--CC-CGA-G--------------------------------------------------------------------CT-T-AA-------------------------------------------------------------------------CT-T-G-GG-AA-C----T-G-C-A-T-T--------T--GA-A-A-C-T-G-GCA--A-G-C---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------T-A-G-A-G-T-C-----T-CG--TA-G-A------------G-GG-G-GG-T----AG--AATT-CCA-G-GT--GT-A-GCG-GTGAAA-TG-CGT-AGAG-A-TC-T-GGA--GG-A-AT-A-CC-GG--T--G--GC-GAA-G--G-C---G----G--C-C-CCCTG------G-AC-GA--------------------------------------------------------------AG-A-C-T--GA--CG-----CT-CA-GG--T-G-CGA--AA-G-C--------------G-TGGG-GAG-C-A-AACA--GG-ATTA-G-ATA-C-----CC-T-G-GTA-G-T----C-CA--C-G-CCG-T-AAA--C-GATG-TC--GA-TT---------T-GG--A--G-G-TT-G-TG-C--C--------------------------------------------------------------------------------------CTT-GA--------------------------------------------------------------------------------------------------------------------------------------------------G-G-C-GT--G-G-C-T-TC-C------GG--A----GC-TAA--CG-C-G-T--T--AA-AT--C----G-ACC-GCC-T-G-GG-GAG-TA---CGG-----C-C--G-C-A-A-GGT-T--AAA-ACTC-AAA---------TGAA-TTG-ACGGG-G-G-CCCG----C-A--C-A-A-GCG-GT-G--G--AG-CA-T--GT-GGT-TT-AATT-C-G-ATG-CAAC-G-CG-A-AG-A-A-CC-TT-A-CC-TACTC-TT-G-AC-A-T-C--------------CAG-A-G-------------A-AC-T-T-T--CC--A-GA-G-A-T--G-G-A--T-T-G-G--T-G-----CC-------------------------------------T--TC-G------------------------------------------GG----A----A---CT-CTG---A--GA---------------------------------------------------C-A-G-G-T-GCTG-CA-TGG-CT--GTC-GTC-A-GC-TC---G-TG-TT-G--TGA-AA-TGT-T-GG-G-TT-AA-GT-CCCGC-AA--------C-GAG-CGC-A-ACC-C-T-TA--TC--C-TTTG--T-T-G-C-C---AG-C-G--G--T-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------TCG------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------G----C----C-G------------G----G---A-A--CT---------------C-A-A-A-G-GA-G--AC-T-G-CCA--G-T------------------------------------G-A---TAA----------------------------------A-C-T-G--G-A-GG-A--AGG-T--GGGG-A-TGAC-GTC--AAGT-C---ATC-A-T-G-G-C-C-CTT----AC-G--AG-T-A-GG-GC-TA-CAC-ACGTG-C--TA--CAATG---G-CGTA-T-A--C-AAA-GA-GA--------------------------------------------------------------------------------------------------A-G-C-G-A--ACCT-G-C--G---------------------------------------A-GG-G-C-----------A--A-G-CG---G----------A--CCT-C------A-T-AAAGT-AC-G-T-C-G-TAG-TCC--------GGA-T-TGGAG-TC--T-GCAA-CT-C-------------------------------------------------------------------------------------------------G-ACTCC-A-T-G-AA-G-TC-GGAAT-CG-C-TA--G-TA-AT-C-G-T----AGA-TC-A-G--A------AT--GCT-AC-G-GT-G-AAT-ACGT-T-CCCGGGCCT-TGTA----CACACCG-CCC-GTC-----A---CA--CCA-TG-GG-A--G---TGG-G-TT-GC-AAA--A-GAA------G--T-AGG-TA-G-C-T-T-AA-C-C-------------------------------------------------------------T-TC-G------------------------------------------------------------------------------------------------------GG-A--GG-G--C---GC-TTA--CC--ACT-T----T-GT..........................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................");
  22                 refSeqs.resize(2);
  23                 refSeqs[1]->setName("S000381740"); refSeqs[1]->setAligned("...............................................................................................................................................a-c-gc--tgg-c--g-gc-a-gg--c----c-t--aacaca-t-gc-a-agt-cga-g-cg----------g-tag-ca-c----------------------------agga-g-ag----------------------------------------------------ctt-g----------------------------------------------------------------------------------ctc-tctg----------------g-gt--g--ac--g--ag-c-gg-c-gg-a--c-------------ggg-tgagt-a--at-gt-c-t-g-gg---a-a--a-ct-g--c-c-tga--tg-g------------------------------------------------------------------a-gg----ggg-at-aa-cta-------------------------c-t-g-----------------------gaa-a---cgg-tag-ctaa-ta---cc-g--c-at-a----------a--------------------c-------------------------------------gt-c-----------------------------------------------------------------------------------------------------------------------t-ac-g--------------------------------------------------------------------------------------------------------------------------------------g-a-c---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------caaa--g-t-g-gg-----g--ga-c--c--------------------------------------------------------------------------------------------------------------------ttc-g----------------------------------------------------------------------------------------------------------------------g-g--cc-tc--a---c-g--------------c----c-a---t-ca-g---at---g-t-----g-ccc-aga--t-ggg--a------tt--a--g-ct-a----g---tagg-t-g-gg-g-t----aat-gg-c-t-c-acct--a-gg-c-g--a-cg-a------------tcc-c-t------ag-ct-g-g-tct-g-ag----a--gg-at--g-ac-c-ag-ccac-a-ctgga--a-c-tg-a-ga-c-ac-g-g-tccaga-ctcc-tac-g--g-g-a-g-gc-a-gc-a-g-tg---gg-g-a-ata-ttgca-c-aa-t-gg--gc-gc-a----a-g-cc-t-ga-tg-ca-gcca-tgcc-g-cg-t---g-t-g--t--ga-a-g--a--a-g-g-cc-----tt-cg---------g-g-t-t-g-t--a---aa-g-cac--------tt-tc-a-g--c-gag----ga-g--g---aa-gggc---gatg-tc----t--t--aa-t---a----c-----gg-c-agc-gca-tt-ga-cg-tt-a-c-tc-g-ca-g---------aa-----------gaagc-acc-gg-c-taa---c--t-ccgt--gcca--g-c---a--gccg---c-gg--ta-at--ac---gg-ag-ggt-gca-a-g-cg-ttaa-t-cgg-aa-tt-a--c-t--gggc-gta----aa-gcgc-ac--g-ca-g-g-c-g------------g--t-tt-g-t-t-aa----g-t-c-a---g-atg-tg-a-aa-tc--cc-cgc-g--------------------------------------------------------------------ct-t-aa-------------------------------------------------------------------------cg-t-g-gg-aa-c----t-g-c-a-t-t--------t--ga-a-a-c-t-g-gca--a-g-c---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------t-a-g-a-g-t-c-----t-cg--ta-g-a------------g-gg-g-gg-t----ag--aatt-cca-g-gt--gt-a-gcg-gtgaaa-tg-cgt-agag-a-tc-t-gga--gg-a-at-a-cc-gg--t--g--gc-gaa-g--g-c---g----g--c-c-ccctg------g-ac-ga--------------------------------------------------------------ag-a-c-t--ga--cg-----ct-ca-gg--t-g-cga--aa-g-c--------------g-tggg-gag-c-a-aaca--gg-atta-g-ata-c-----cc-t-g-gta-g-t----c-ca--c-g-ctg-t-aaa--c-gatg-tc--ga-tt---------t-gg--a--g-g-tt-g-tg-c--c--------------------------------------------------------------------------------------ctt-ga--------------------------------------------------------------------------------------------------------------------------------------------------g-g-c-gt--g-g-c-t-tc-c------gg--a----gc-taa--cg-c-g-t--t--aa-at--c----g-acc-gcc-t-g-gg-gag-ta---cgg-----c-c--g-c-a-a-ggt-t--aaa-actc-aaa---------tgaa-ttg-acggg-g-g-cccg----c-a--c-a-a-gcg-gt-g--g--ag-ca-t--gt-ggt-tt-aatt-c-g-atg-caac-g-cg-a-ag-a-a-cc-tt-a-cc-tactc-tt-g-ac-a-t-c--------------cag-a-g-------------a-ac-t-t-t--cc--a-ga-g-a-t--g-g-a--t-t-g-g--t-g-----cc-------------------------------------t--tc-g------------------------------------------gg----a----a---ct-ctg---a--ga---------------------------------------------------c-a-g-g-t-gctg-ca-tgg-ct--gtc-gtc-a-gc-tc---g-tg-tt-g--tga-aa-tgt-t-gg-g-tt-aa-gt-cccgc-aa--------c-gag-cgc-a-acc-c-t-ta--tc--c-tttg--t-t-g-c-c---ag-c-g--a--t-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------tcg------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------g----t----c-g------------g----g---a-a--ct---------------c-a-a-a-g-ga-g--ac-t-g-ccg--g-t------------------------------------g-a---taa----------------------------------a-c-c-g--g-a-gg-a--agg-t--gggg-a-tgac-gtc--aagt-c---atc-a-t-g-g-c-c-ctt----ac-g--ag-t-a-gg-gc-ta-cac-acgtg-c--ta--caatg---g-cgta-t-a--c-aaa-ga-ga--------------------------------------------------------------------------------------------------a-g-c-g-a--a-ctcg-c--g---------------------------------------a-ga-g-c-----------a--a-g-cg---g----------a--cct-c------a-t-aaagt-ac-g-t-c-g-tag-tcc--------gga-t-tggag-tc--t-gcaa-ct-c-------------------------------------------------------------------------------------------------g-actcc-a-t-g-aa-g-tc-ggaat-cg-c-ta--g-ta-at-c-g-t----aga-tc-a-g--a------at--gct-ac-g-gt-g-aat-acgt-t-cccgggcct-tgta----cacaccg-ccc-gtc-----a---ca--cca-tg-gg-a--g---tgg-g-tt-gc-aaa--a-gaa------g--t-agg-ta-g-c-t-t-aa-c-c-------------------------------------------------------------t-tc-g------------------------------------------------------------------------------------------------------gg-a--gg-g--c---gc-tta--cc--act-t----t-gtg-at-tca------------------------t.........................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................");
  24                 refSeqs[0]->setName("7000004131500404"); refSeqs[0]->setAligned(".........................................................................................................................................AT-TGAA-C-GC--TGG-C--G-GC-A-GG--C----C-T--AACACA-T-GC-A-AGT-CGA-G-CG----------G-CAG-CG-G----------------------------AAAG-A-AG----------------------------------------------------CTT-G---------------------------------------------------------------------------------ACTT-CTTT----------------G-CC--G--GC--G--AG-C-GG-C-GG-A--C-------------GGG-TGAGT-A--AT-GT-C-T-G-GG---G-A--T-CT-G--C-C-CGA--TG-G------------------------------------------------------------------A-GG----GGG-AT-AA-CTA-------------------------C-T-G-----------------------GAA-A---CGG-TAG-CTAA-TA---CC-G--C-AT-A----------A--------------------C-------------------------------------GT-C-----------------------------------------------------------------------------------------------------------------------G-CA-A--------------------------------------------------------------------------------------------------------------------------------------G-A-C---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CAAA--G-T-G-GG-----G--GA-C--C--------------------------------------------------------------------------------------------------------------------TTC-G----------------------------------------------------------------------------------------------------------------------G-G--CC-TC--A---C-A--------------C----C-A---T-CG-G---AT---G-A-----A-CCC-AGA--T-GGG--A------TT--A--G-CT-A----G---TAGG-T-G-GG-G-T----AAT-GG-C-T-C-ACCT--A-GG-C-G--A-CG-A------------TCC-C-T------AG-CT-G-G-TCT-G-AG----A--GG-AT--G-AC-C-AG-CCAC-A-CTGGA--A-C-TG-A-GA-C-AC-G-G-TCCAGA-CTCC-TAC-G--G-G-A-G-GC-A-GC-A-G-TG---GG-G-A-ATA-TTGCA-C-AA-T-GG--GG-GA-A----A-C-CC-T-GA-TG-CA-GCCA-TGCC-G-CG-T---G-T-G--T--GA-A-G--A--A-G-G-CC-----TT-CG---------G-G-T-T-G-T--A---AA-G-CAC--------TT-TC-A-G--C-GGG----GA-A--G---AA-GGCG---TT-A-GC---GT--T--AA-C---A----G-----CG-C-TAT-CGA-TT-GA-CG-TT-A-C-CT-G-CA-G---------AA-----------GAAGC-ACC-GG-C-TAA---C--T-CCGT--GCCA--G-C---A--GCCG---C-GG--TA-AT--AC---GG-AG-GGT-GCA-A-G-CG-TTAA-T-CGG-AA-TT-A--C-T--GGGC-GTA----AA-GCGT-AC--G-CA-G-G-C-G------------G--T-CT-G-T-T-AA----G-T-C-A---G-ATG-TG-A-AA-TC--CC-CGG-G--------------------------------------------------------------------CT-T-AA-------------------------------------------------------------------------CC-T-G-GG-AA-C----T-G-C-A-T-T--------T--GA-A-A-C-T-G-GCA--G-G-C---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------T-A-G-A-G-T-C-----T-CG--TA-G-A------------G-GG-G-GG-T----AG--AATT-CCA-G-GT--GT-A-GCG-GTGAAA-TG-CGT-AGAG-A-TC-T-GGA--GG-A-AT-A-CC-GG--T--G--GC-GAA-G--G-C---G----G--C-C-CCCTG------G-AC-GA--------------------------------------------------------------AG-A-C-T--GA--CG-----CT-CA-GG--T-A-CGA--AA-G-C--------------G-TGGG-GAG-C-A-AACA--GG-ATTA-G-ATA-C-----CC-T-G-GTA-G-T----C-CA--C-G-CTG-T-AAA--C-GATG-TC--GA-TT---------T-GA--A--G-G-TT-G-TG-G--C--------------------------------------------------------------------------------------CTT-GA--------------------------------------------------------------------------------------------------------------------------------------------------G-C-T-GT--G-G-C-T-TT-C------GG--A----GC-TAA--CG-C-G-T--T--AA-AT--C----G-ACC-GCC-T-G-GG-GAG-TA---CGG-----C-C--G-C-A-A-GGT-T--AAA-ACTC-AAA---------TGAA-TTG-ACGGG-G-G-CCCG----C-A--C-A-A-GCG-GT-G--G--AG-CA-T--GT-GGT-TT-AATT-C-G-ATG-CAAC-G-CG-A-AG-A-A-CC-TT-A-CC-TACTC-TT-G-AC-A-T-C--------------CAG-A-G-------------A-AC-T-T-G--GC--A-GA-G-A-T--G-C-C--T-T-G-G--T-G-----CC-------------------------------------T--TC-G------------------------------------------GG----A----G---CT-CTG---A--GA---------------------------------------------------C-A-G-G-T-GCTG-CA-TGG-CT--GTC-GTC-A-GC-TC---G-TG-TT-G--TGA-AA-TGT-T-GG-G-TT-AA-GT-CCCGC-AA--------C-GAG-CGC-A-ACC-C-T-TA--TC--C-TTTG--T-T-G-C-C---AG-C-G--A--T-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------TTG------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------G----T----C-G------------G----G---A-A--CT---------------C-A-A-A-G-GA-G--AC-T-G-CCG--G-T------------------------------------G-A---TAA----------------------------------A-C-C-G--G-A-GG-A--AGG-T--GGGG-A-TGAC-GTC--AAGT-C---ATC-A-T-G-G-C-C-CTT----AC-G--AG-T-A-GG-GC-TA-CAC-ACGTG-C--TA--CAATG---G-CGCA-T-A--C-AAA-GA-GA--------------------------------------------------------------------------------------------------A-G-C-G-A--T-CTCG-C--G---------------------------------------A-GA-G-T-----------C--A-G-CG---G----------A--CCT-C------A-C-AAAGT-GC-G-T-C-G-TAG-TCC--------GGA-T-TGGAG-TC--T-GCAA-CT-C-------------------------------------------------------------------------------------------------G-ACTCC-A-T-G-AA-G-TC-GGAAT-CG-C-TA--G-TA-AT-C-G-T----GGA-TC-A-G--A------AT--GCC-AC-G-GT-G-AAT-ACGT-T-CCTGGGCCT-TGTA----CACACCG-CCC-GTC-----A---CA--CCA-TG-GG-A--G---TGG-G-TT-GC-AAA--A-GAA------G--T-AGG-TA-G-C-T-T-AA-C-C-------------------------------------------------------------T-TC-G------------------------------------------------------------------------------------------------------GG-A--GG-G--C---GC-TTA--CC--ACT-T----T-GTG-AT-TCA------------------------TG--ACT-GGGG-TG-AAG-TCGTAACAA-GGTAA-CCGT-AGGGGAA-CCT......................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................");
  25                 for (int i = 0; i < refSeqs.size(); i++) {
  26                         string newAligned = "";
  27                         for (int j = 0; j < refSeqs[i]->getAligned().length(); j++) {
  28                                 newAligned += toupper(refSeqs[i]->getAligned()[j]);
  29                         }
  30                         refSeqs[i]->setAligned(newAligned);
  31                 }*/
  32
  33                 for (int i = 0; i < refSeqs.size(); i++) {
  34
  35                         for (int j = i+1; j < refSeqs.size(); j++) {
  36
  37                                 if (m->control_pressed) { return "no";  }
  38
  39                                 //make copies of query and each parent because runBellerophon removes gaps and messes them up
  40                                 Sequence* q = new Sequence(query->getName(), query->getAligned());
  41                                 Sequence* leftParent = new Sequence(refSeqs[i]->getName(), refSeqs[i]->getAligned());
  42                                 Sequence* rightParent = new Sequence(refSeqs[j]->getName(), refSeqs[j]->getAligned());
  43
  44                                 map<int, int> spots;  //map from spot in original sequence to spot in filtered sequence for query and both parents
  45                                 vector<data_struct> divs = runBellerophon(q, leftParent, rightParent, spots);
  46                                 //cout << divs.size() << endl;
  47                                 if (m->control_pressed) {
  48                                         delete q;
  49                                         delete leftParent;
  50                                         delete rightParent;
  51                                         return "no";
  52                                 }
  53
  54 //                              cout << divs.size() << endl;
  55                                 vector<data_struct> selectedDivs;
  56                                 for (int k = 0; k < divs.size(); k++) {
  57
  58                                         vector<snps> snpsLeft = getSNPS(divs[k].parentA.getAligned(), divs[k].querySeq.getAligned(), divs[k].parentB.getAligned(), divs[k].winLStart, divs[k].winLEnd);
  59                                         vector<snps> snpsRight = getSNPS(divs[k].parentA.getAligned(), divs[k].querySeq.getAligned(), divs[k].parentB.getAligned(), divs[k].winRStart, divs[k].winREnd);
  60
  61                                         if (m->control_pressed) {
  62                                                 delete q;
  63                                                 delete leftParent;
  64                                                 delete rightParent;
  65                                                 return "no";
  66                                         }
  67
  68                                         int numSNPSLeft = snpsLeft.size();
  69                                         int numSNPSRight = snpsRight.size();
  70
  71                                         //require at least 3 SNPs on each side of the break
  72 //                                      if ((numSNPSLeft >= 3) && (numSNPSRight >= 3)) {
  73                                         if ((numSNPSLeft >= 4) && (numSNPSRight >= 4)) {
  74
  75                                                 //removed in 12/09 version of chimeraSlayer
  76                                                 //int winSizeLeft = divs[k].winLEnd - divs[k].winLStart + 1;
  77                                                 //int winSizeRight = divs[k].winREnd - divs[k].winRStart + 1;
  78
  79                                                 //float snpRateLeft = numSNPSLeft / (float) winSizeLeft;
  80                                                 //float snpRateRight = numSNPSRight / (float) winSizeRight;
  81                                                 //float logR = log(snpRateLeft / snpRateRight) / log(2.0);
  82
  83                                                 // do not accept excess snp ratio on either side of the break
  84                                                 //if (abs(logR) < 1 ) {
  85
  86                                                         float BS_A, BS_B;
  87                                                         bootstrapSNPS(snpsLeft, snpsRight, BS_A, BS_B, iters);
  88
  89                                                         if (m->control_pressed) {
  90                                                                 delete q;
  91                                                                 delete leftParent;
  92                                                                 delete rightParent;
  93                                                                 return "no";
  94                                                         }
  95
  96                                                         divs[k].bsa = BS_A;
  97                                                         divs[k].bsb = BS_B;
  98
  99                                                         divs[k].bsMax = max(BS_A, BS_B);
 100
 101                                                         divs[k].chimeraMax = max(divs[k].qla_qrb, divs[k].qlb_qra);
 102
 103                                                         //so results reflect orignal alignment
 104                                                         divs[k].winLStart = spots[divs[k].winLStart];
 105                                                         divs[k].winLEnd = spots[divs[k].winLEnd];
 106                                                         divs[k].winRStart = spots[divs[k].winRStart];
 107                                                         divs[k].winREnd = spots[divs[k].winREnd];
 108
 109                                                         selectedDivs.push_back(divs[k]);
 110                                                 //}
 111                                         }
 112                                 }
 113
 114                                 //save selected
 115                                 for (int m = 0; m < selectedDivs.size(); m++) {  all.push_back(selectedDivs[m]);        }
 116
 117                                 delete q;
 118                                 delete leftParent;
 119                                 delete rightParent;
 120                         }
 121                 }
 122
 123                 // compute bootstrap support
 124                 if (all.size() > 0) {
 125                         //sort them
 126                         sort(all.begin(), all.end(), compareDataStruct);
 127                         reverse(all.begin(), all.end());
 128
 129                         outputResults = all;
 130                         return "yes";
 131                 }
 132                 else {
 133                         outputResults = all;
 134                         return "no";
 135                 }
 136         }
 137         catch(exception& e) {
 138                 m->errorOut(e, "Slayer", "getResults");
 139                 exit(1);
 140         }
 141 }
 142 /***********************************************************************/
 143 vector<data_struct> Slayer::runBellerophon(Sequence* q, Sequence* pA, Sequence* pB, map<int, int>& spots) {
 144         try{
 145
 146                 vector<data_struct> data;
 147
 148                 //vertical filter
 149                 vector<Sequence*> temp;
 150                 temp.push_back(q); temp.push_back(pA); temp.push_back(pB);
 151
 152                 //maps spot in new alignment to spot in alignment before filter
 153                 spots = verticalFilter(temp);  //fills baseSpots
 154
 155                 //get these to avoid numerous function calls
 156                 string query = q->getAligned();
 157                 string parentA = pA->getAligned();
 158                 string parentB = pB->getAligned();
 159                 int length = query.length();
 160 /*cout << q->getName() << endl << q->getAligned() << endl << endl;
 161 cout << pA->getName() << endl << pA->getAligned() << endl << endl;
 162 cout << pB->getName() << endl << pB->getAligned() << endl << endl;
 163 cout << " length = " << length << endl;
 164 cout << q->getName() << endl;
 165 cout << pA->getName() << '\t';
 166 cout << pB->getName() << endl;*/
 167
 168                 //check window size
 169                 if (length < (2*windowSize+windowStep)) {
 170 //                      m->mothurOut("Your window size is too large for " + q->getName() + ". I will make the window size " + toString(length/4) + " which is 1/4 the filtered length."); m->mothurOutEndLine();
 171                         windowSize = length / 4;
 172                 }
 173
 174                 for (int i = windowSize-1; i <= (length - windowSize); i += windowStep) {
 175
 176                         if (m->control_pressed) { return data; }
 177
 178                         int breakpoint = i;
 179                         int leftLength = breakpoint + 1;
 180                         int rightLength = length - leftLength;
 181
 182                         float QLA = computePercentID(query, parentA, 0, breakpoint);
 183                         float QRB = computePercentID(query, parentB, breakpoint+1, length - 1);
 184
 185                         float QLB = computePercentID(query, parentB, 0, breakpoint);
 186                         float QRA = computePercentID(query, parentA, breakpoint+1, length - 1);
 187
 188                         float LAB = computePercentID(parentA, parentB, 0, breakpoint);
 189                         float RAB = computePercentID(parentA, parentB, breakpoint+1, length - 1);
 190
 191                         float AB = ((LAB*leftLength) + (RAB*rightLength)) / (float) length;
 192                         float QA = ((QLA*leftLength) + (QRA*rightLength)) / (float) length;
 193                         float QB = ((QLB*leftLength) + (QRB*rightLength)) / (float) length;
 194
 195                         float QLA_QRB = ((QLA*leftLength) + (QRB*rightLength)) / (float) length;
 196                         float QLB_QRA = ((QLB*leftLength) + (QRA*rightLength)) / (float) length;
 197
 198                         //in original and not used
 199                         //float avgQA_QB = ((QA*leftLength) + (QB*rightLength)) / (float) length;
 200
 201                         float divR_QLA_QRB = min((QLA_QRB/QA), (QLA_QRB/QB));
 202                         float divR_QLB_QRA = min((QLB_QRA/QA), (QLB_QRA/QB));
 203 //cout << leftLength << '\t' << rightLength << '\t' << QLA << '\t' << QRB << '\t' << QLB << '\t' << QRA  << '\t' << LAB << '\t' << RAB << '\t' << AB << '\t' << QA << '\t' << QB << '\t' << QLA_QRB << '\t' <<  QLB_QRA <<    endl;
 204
 205 //cout << divRThreshold << endl;
 206 //cout << breakpoint << '\t' << divR_QLA_QRB << '\t' << divR_QLB_QRA << endl;
 207                         //is one of them above the
 208                         if (divR_QLA_QRB >= divRThreshold || divR_QLB_QRA >= divRThreshold) {
 209
 210                                 if (((QLA_QRB > QA) && (QLA_QRB > QB) && (QLA >= parentFragmentThreshold) && (QRB >= parentFragmentThreshold))  ||
 211                                         ((QLB_QRA > QA) && (QLB_QRA > QB) && (QLB >=parentFragmentThreshold) && (QRA >= parentFragmentThreshold)))  {
 212
 213                                         data_struct member;
 214
 215                                         member.divr_qla_qrb = divR_QLA_QRB;
 216                                         member.divr_qlb_qra = divR_QLB_QRA;
 217                                         member.qla_qrb = QLA_QRB;
 218                                         member.qlb_qra = QLB_QRA;
 219                                         member.qla = QLA;
 220                                         member.qrb = QRB;
 221                                         member.ab = AB;
 222                                         member.qa = QA;
 223                                         member.qb = QB;
 224                                         member.lab = LAB;
 225                                         member.rab = RAB;
 226                                         member.qra = QRA;
 227                                         member.qlb = QLB;
 228                                         member.winLStart = 0;
 229                                         member.winLEnd = breakpoint;
 230                                         member.winRStart = breakpoint+1;
 231                                         member.winREnd = length-1;
 232                                         member.querySeq = *(q);
 233                                         member.parentA = *(pA);
 234                                         member.parentB = *(pB);
 235                                         member.bsa = 0;
 236                                         member.bsb = 0;
 237                                         member.bsMax = 0;
 238                                         member.chimeraMax = 0;
 239
 240                                         data.push_back(member);
 241
 242                                 }//if
 243                         }//if
 244                 }//for
 245
 246                 return data;
 247
 248         }
 249         catch(exception& e) {
 250                 m->errorOut(e, "Slayer", "runBellerophon");
 251                 exit(1);
 252         }
 253 }
 254 /***********************************************************************/
 255 vector<snps> Slayer::getSNPS(string parentA, string query, string parentB, int left, int right) {
 256         try {
 257
 258                 vector<snps> data;
 259 //cout << left << '\t' << right << endl;
 260                 for (int i = left; i <= right; i++) {
 261
 262                         char A = parentA[i];
 263                         char Q = query[i];
 264                         char B = parentB[i];
 265
 266                         if ((A != Q) || (B != Q)) {
 267 //cout << "not equal " << Q << '\t' << A << '\t' << B << endl;
 268
 269                                 //ensure not neighboring a gap. change to 12/09 release of chimeraSlayer - not sure what this adds, but it eliminates alot of SNPS
 270                                 if (
 271                                         //did query loose a base here during filter??
 272                                         ( i == 0 || abs (baseSpots[0][i] - baseSpots[0][i-1]) == 1) &&
 273                                         ( i == query.length() || abs (baseSpots[0][i] - baseSpots[0][i+1]) == 1)
 274                                         &&
 275                                         //did parentA loose a base here during filter??
 276                                         ( i == 0 || abs (baseSpots[1][i] - baseSpots[1][i-1]) == 1) &&
 277                                         ( i == parentA.length() || abs (baseSpots[1][i] - baseSpots[1][i+1]) == 1)
 278                                         &&
 279                                         //did parentB loose a base here during filter??
 280                                         ( i == 0 || abs (baseSpots[2][i] - baseSpots[2][i-1]) == 1) &&
 281                                         ( i == parentB.length() || abs (baseSpots[2][i] - baseSpots[2][i+1]) == 1)
 282                                         )
 283                                 {
 284
 285                                         snps member;
 286                                         member.queryChar = Q;
 287                                         member.parentAChar = A;
 288                                         member.parentBChar = B;
 289 //cout << "not neighboring a gap " << Q << '\t' << A << '\t' << B << '\t' << baseSpots[0][i] << '\t' << baseSpots[0][i+1] << '\t' << baseSpots[0][i-1] << '\t' << baseSpots[1][i] << '\t' << baseSpots[1][i+1] << '\t' << baseSpots[1][i-1] << '\t' << baseSpots[2][i] << '\t' << baseSpots[2][i+1] << '\t' << baseSpots[2][i-1] << endl;
 290                                         data.push_back(member);
 291                                 }
 292                         }
 293 //                      cout << i << '\t' << data.size() << endl;
 294                 }
 295
 296                 return data;
 297
 298         }
 299         catch(exception& e) {
 300                 m->errorOut(e, "Slayer", "getSNPS");
 301                 exit(1);
 302         }
 303 }
 304 /***********************************************************************/
 305 int Slayer::bootstrapSNPS(vector<snps> left, vector<snps> right, float& BSA, float& BSB, int numIters) {
 306         try {
 307
 308                 srand((unsigned)time( NULL ));
 309
 310                 int count_A = 0; // sceneario QLA,QRB supported
 311                 int count_B = 0; // sceneario QLB,QRA supported
 312
 313                 int numLeft = max(1, int(left.size() * percentSNPSample/(float)100 + 0.5));
 314                 int numRight = max(1, int(right.size() * percentSNPSample/(float)100 + 0.5));
 315
 316                 for (int i = 0; i < numIters; i++) {
 317                         //random sampling with replacement.
 318
 319                         if (m->control_pressed) { return 0;  }
 320
 321                         vector<snps> selectedLeft;
 322
 323                         for (int j = 0; j < numLeft; j++) {
 324                                 int index = int(rand() % left.size());
 325                                 selectedLeft.push_back(left[index]);
 326                         }
 327
 328                         vector<snps> selectedRight;
 329                         for (int j = 0; j < numRight; j++) {
 330                                 int index = int(rand() % right.size());
 331                                 selectedRight.push_back(right[index]);
 332                         }
 333
 334                         /* A  ------------------------------------------
 335                         #       QLA                     QRA
 336                         # Q  ------------------------------------------
 337                         #                      |
 338                         #                      |
 339                         # Q  ------------------------------------------
 340                         #       QLB                     QRB
 341                         # B  ------------------------------------------ */
 342
 343
 344                         float QLA = snpQA(selectedLeft);
 345                         float QRA = snpQA(selectedRight);
 346
 347                         float QLB = snpQB(selectedLeft);
 348                         float QRB = snpQB(selectedRight);
 349
 350                         //in original - not used - not sure why?
 351                         //float ALB = snpAB(selectedLeft);
 352                         //float ARB = snpAB(selectedRight);
 353
 354                         if ((QLA > QLB) && (QRB > QRA)) {
 355                                 count_A++;
 356                         }
 357
 358                         if ((QLB > QLA) && (QRA > QRB)) {
 359                                 count_B++;
 360                         }
 361
 362 //cout << "selected left snp: \n";
 363 //for (int j = 0; j < selectedLeft.size(); j++) {  cout << selectedLeft[j].parentAChar;  }
 364 //cout << endl;
 365 //for (int j = 0; j < selectedLeft.size(); j++) {  cout << selectedLeft[j].queryChar;  }
 366 //cout << endl;
 367 //for (int j = 0; j < selectedLeft.size(); j++) {  cout << selectedLeft[j].parentBChar;  }
 368 //cout << endl;
 369 //cout << "selected right snp: \n";
 370 //for (int j = 0; j < selectedRight.size(); j++) {  cout << selectedRight[j].parentAChar;  }
 371 //cout << endl;
 372 //for (int i = 0; i < selectedRight.size(); i++) {  cout << selectedRight[i].queryChar;  }
 373 //cout << endl;
 374 //for (int i = 0; i < selectedRight.size(); i++) {  cout << selectedRight[i].parentBChar;  }
 375 //cout << endl;
 376                 }
 377
 378
 379
 380
 381                 BSA = (float) count_A / (float) iters * 100;
 382                 BSB = (float) count_B / (float) iters * 100;
 383 //cout << "bsa = " << BSA << " bsb = " << BSB << endl;
 384
 385                 //run borderline bootstrap values longer
 386                 //if (numIters < 1000) {
 387                         //are you within 10 points of min bootstrap value cutoff
 388                 //      if (((abs((double)(BSA - minBS))) <= 5) || ((abs((double)(BSB - minBS))) <= 5)) {
 389                 //              m->mothurOut("extending bootstrap for " + myQuery.getName()); m->mothurOutEndLine();
 390                 //              bootstrapSNPS(left, right, BSA, BSB, 1000);
 391                 //      }
 392                 //}
 393
 394                 return 0;
 395
 396         }
 397         catch(exception& e) {
 398                 m->errorOut(e, "Slayer", "bootstrapSNPS");
 399                 exit(1);
 400         }
 401 }
 402 /***********************************************************************/
 403 float Slayer::snpQA(vector<snps> data) {
 404         try {
 405
 406                 int numIdentical = 0;
 407
 408                 for (int i = 0; i < data.size(); i++) {
 409                         if (data[i].parentAChar == data[i].queryChar) {
 410                                 numIdentical++;
 411                         }
 412                 }
 413
 414                 float percentID = (numIdentical / (float) data.size()) * 100;
 415
 416                 return percentID;
 417         }
 418         catch(exception& e) {
 419                 m->errorOut(e, "Slayer", "snpQA");
 420                 exit(1);
 421         }
 422 }
 423 /***********************************************************************/
 424 float Slayer::snpQB(vector<snps> data) {
 425         try {
 426
 427                 int numIdentical = 0;
 428
 429                 for (int i = 0; i < data.size(); i++) {
 430                         if (data[i].parentBChar == data[i].queryChar) {
 431                                 numIdentical++;
 432                         }
 433                 }
 434
 435                 float percentID = (numIdentical / (float) data.size()) * 100;
 436
 437                 return percentID;
 438
 439         }
 440         catch(exception& e) {
 441                 m->errorOut(e, "Slayer", "snpQB");
 442                 exit(1);
 443         }
 444 }
 445 /***********************************************************************/
 446 float Slayer::snpAB(vector<snps> data) {
 447         try {
 448                 int numIdentical = 0;
 449
 450                 for (int i = 0; i < data.size(); i++) {
 451                         if (data[i].parentAChar == data[i].parentBChar) {
 452                                 numIdentical++;
 453                         }
 454                 }
 455
 456                 float percentID = (numIdentical / (float) data.size()) * 100;
 457
 458                 return percentID;
 459
 460         }
 461         catch(exception& e) {
 462                 m->errorOut(e, "Slayer", "snpAB");
 463                 exit(1);
 464         }
 465 }
 466 /***********************************************************************/
 467 float Slayer::computePercentID(string queryFrag, string parent, int left, int right) {
 468         try {
 469                 int total = 0;
 470                 int matches = 0;
 471
 472                 for (int i = left; i <= right; i++) {
 473                         total++;
 474                         if (queryFrag[i] == parent[i]) {
 475                                 matches++;
 476                         }
 477                 }
 478
 479                 float percentID =( matches/(float)total) * 100;
 480
 481                 return percentID;
 482         }
 483         catch(exception& e) {
 484                 m->errorOut(e, "Slayer", "computePercentID");
 485                 exit(1);
 486         }
 487 }
 488 /***********************************************************************/
 489 //remove columns that contain any gaps
 490 map<int, int> Slayer::verticalFilter(vector<Sequence*> seqs) {
 491         try {
 492                 //find baseSpots
 493                 baseSpots.clear();
 494                 baseSpots.resize(3);  //query, parentA, parentB
 495
 496                 vector<int> gaps;       gaps.resize(seqs[0]->getAligned().length(), 0);
 497
 498                 string filterString = (string(seqs[0]->getAligned().length(), '1'));
 499
 500                 //for each sequence
 501                 for (int i = 0; i < seqs.size(); i++) {
 502
 503                         string seqAligned = seqs[i]->getAligned();
 504
 505                         for (int j = 0; j < seqAligned.length(); j++) {
 506                                 //if this spot is a gap
 507                                 if ((seqAligned[j] == '-') || (seqAligned[j] == '.') || (toupper(seqAligned[j]) == 'N'))        {   gaps[j]++;  }
 508                         }
 509                 }
 510
 511                 //zero out spot where any sequences have blanks
 512                 int numColRemoved = 0;
 513                 int count = 0;
 514                 map<int, int> maskMap; maskMap.clear();
 515
 516                 for(int i = 0; i < seqs[0]->getAligned().length(); i++){
 517                         if(gaps[i] != 0)        {       filterString[i] = '0';  numColRemoved++;  }
 518                         else {
 519                                 maskMap[count] = i;
 520                                 count++;
 521                         }
 522                 }
 523
 524                 //for each sequence
 525                 for (int i = 0; i < seqs.size(); i++) {
 526
 527                         string seqAligned = seqs[i]->getAligned();
 528                         string newAligned = "";
 529
 530                         int baseCount = 0;
 531                         int count = 0;
 532                         for (int j = 0; j < seqAligned.length(); j++) {
 533                                 //are you a base
 534                                 if ((seqAligned[j] != '-') && (seqAligned[j] != '.') && (toupper(seqAligned[j]) != 'N'))        { baseCount++; }
 535
 536                                 //if this spot is not a gap
 537                                 if (filterString[j] == '1') {
 538                                         newAligned += seqAligned[j];
 539                                         baseSpots[i][count] = baseCount;
 540                                         count++;
 541                                 }
 542                         }
 543
 544                         seqs[i]->setAligned(newAligned);
 545                 }
 546
 547                 return maskMap;
 548         }
 549         catch(exception& e) {
 550                 m->errorOut(e, "Slayer", "verticalFilter");
 551                 exit(1);
 552         }
 553 }
 554 /***********************************************************************/