71 lines
2.0 KiB
C++
71 lines
2.0 KiB
C++
#include "MainTools.h"
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#include "Basevector.h"
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#include "lookup/LookAlign.h"
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#include "lookup/SerialQltout.h"
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unsigned int MatchingEnd(look_align &la, vecbasevector &candidates, vecbasevector &ref) {
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//la.PrintParseable(cout);
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for (int i = 0; i < candidates.size(); i++) {
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look_align newla = la;
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if (newla.rc1) { candidates[i].ReverseComplement(); }
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newla.ResetFromAlign(newla.a, candidates[i], ref[la.target_id]);
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//newla.PrintParseable(cout, &candidates[i], &ref[newla.target_id]);
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//cout << newla.Errors() << " " << la.Errors() << endl;
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if (newla.Errors() == la.Errors()) {
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return i;
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}
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}
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//FatalErr("Query id " + ToString(la.query_id) + " had no matches.");
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return candidates.size() + 1;
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}
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int main(int argc, char **argv) {
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RunTime();
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BeginCommandArguments;
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CommandArgument_String(ALIGNS);
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CommandArgument_String(FASTB_END_1);
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CommandArgument_String(FASTB_END_2);
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CommandArgument_String(REFERENCE);
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CommandArgument_String(ALIGNS_END_1_OUT);
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CommandArgument_String(ALIGNS_END_2_OUT);
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EndCommandArguments;
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vecbasevector ref(REFERENCE);
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vecbasevector reads1(FASTB_END_1);
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vecbasevector reads2(FASTB_END_2);
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ofstream aligns1stream(ALIGNS_END_1_OUT.c_str());
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ofstream aligns2stream(ALIGNS_END_2_OUT.c_str());
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basevector bv;
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SerialQltout sqltout(ALIGNS);
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look_align la;
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while (sqltout.Next(la)) {
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vecbasevector candidates(2);
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candidates[0] = reads1[la.query_id];
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candidates[1] = reads2[la.query_id];
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unsigned int matchingend = MatchingEnd(la, candidates, ref);
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if (matchingend < 2) {
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bv = (matchingend == 0) ? reads1[la.query_id] : reads2[la.query_id];
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//la.PrintParseable(cout, &bv, &ref[la.target_id]);
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la.PrintParseable(((matchingend == 0) ? aligns1stream : aligns2stream), &bv, &ref[la.target_id]);
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}
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}
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aligns1stream.close();
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aligns2stream.close();
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return 0;
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}
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