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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,70 @@ | ||
| #include "MainTools.h" | ||
| #include "Basevector.h" | ||
| #include "lookup/LookAlign.h" | ||
| #include "lookup/SerialQltout.h" | ||
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| unsigned int MatchingEnd(look_align &la, vecbasevector &candidates, vecbasevector &ref) { | ||
| //la.PrintParseable(cout); | ||
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| for (int i = 0; i < candidates.size(); i++) { | ||
| look_align newla = la; | ||
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| if (newla.rc1) { candidates[i].ReverseComplement(); } | ||
| newla.ResetFromAlign(newla.a, candidates[i], ref[la.target_id]); | ||
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| //newla.PrintParseable(cout, &candidates[i], &ref[newla.target_id]); | ||
| //cout << newla.Errors() << " " << la.Errors() << endl; | ||
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| if (newla.Errors() == la.Errors()) { | ||
| return i; | ||
| } | ||
| } | ||
|
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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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| int main(int argc, char **argv) { | ||
| RunTime(); | ||
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| BeginCommandArguments; | ||
| CommandArgument_String(ALIGNS); | ||
| CommandArgument_String(FASTB_END_1); | ||
| CommandArgument_String(FASTB_END_2); | ||
| CommandArgument_String(REFERENCE); | ||
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| CommandArgument_String(ALIGNS_END_1_OUT); | ||
| CommandArgument_String(ALIGNS_END_2_OUT); | ||
| EndCommandArguments; | ||
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| vecbasevector ref(REFERENCE); | ||
| vecbasevector reads1(FASTB_END_1); | ||
| vecbasevector reads2(FASTB_END_2); | ||
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| ofstream aligns1stream(ALIGNS_END_1_OUT.c_str()); | ||
| ofstream aligns2stream(ALIGNS_END_2_OUT.c_str()); | ||
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| basevector bv; | ||
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| SerialQltout sqltout(ALIGNS); | ||
| look_align la; | ||
| while (sqltout.Next(la)) { | ||
| vecbasevector candidates(2); | ||
| candidates[0] = reads1[la.query_id]; | ||
| candidates[1] = reads2[la.query_id]; | ||
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| unsigned int matchingend = MatchingEnd(la, candidates, ref); | ||
| if (matchingend < 2) { | ||
| bv = (matchingend == 0) ? reads1[la.query_id] : reads2[la.query_id]; | ||
|
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| //la.PrintParseable(cout, &bv, &ref[la.target_id]); | ||
| la.PrintParseable(((matchingend == 0) ? aligns1stream : aligns2stream), &bv, &ref[la.target_id]); | ||
| } | ||
| } | ||
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| aligns1stream.close(); | ||
| aligns2stream.close(); | ||
|
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| return 0; | ||
| } |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,21 @@ | ||
| CXX=g++ | ||
| CXXFLAGS=-g -Wall -O2 -m64 -fPIC | ||
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| .cpp.o: | ||
| $(CXX) -c $(CXXFLAGS) -I$(BWA_HOME) -I$(JAVA_INCLUDE) $< -o $@ | ||
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| all: init lib | ||
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| init: | ||
| @echo Please make sure the following platforms are set correctly on your machine. | ||
| @echo BWA_HOME=$(BWA_HOME) | ||
| @echo JAVA_INCLUDE=$(JAVA_INCLUDE) | ||
| @echo TARGET_LIB=$(TARGET_LIB) | ||
| @echo EXTRA_LIBS=$(EXTRA_LIBS) | ||
| @echo LIBTOOL_COMMAND=$(LIBTOOL_COMMAND) | ||
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| lib: org_broadinstitute_sting_alignment_bwa_c_BWACAligner.o bwa_gateway.o | ||
| $(LIBTOOL_COMMAND) $? -o $(TARGET_LIB) -L$(BWA_HOME) -lbwacore $(EXTRA_LIBS) | ||
|
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||
| clean: | ||
| rm *.o libbwa.* |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,7 @@ | ||
| #!/bin/sh | ||
| export BWA_HOME="/humgen/gsa-scr1/hanna/src/bwa-trunk/bwa" | ||
| export JAVA_INCLUDE="/broad/tools/Linux/x86_64/pkgs/jdk_1.6.0_12/include -I/broad/tools/Linux/x86_64/pkgs/jdk_1.6.0_12/include/linux" | ||
| export TARGET_LIB="libbwa.so" | ||
| export EXTRA_LIBS="-lc -lz -lstdc++ -lpthread" | ||
| export LIBTOOL_COMMAND="g++ -shared -Wl,-soname,libbwa.so" | ||
| make |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,7 @@ | ||
| #!/bin/sh | ||
| export BWA_HOME="/Users/mhanna/src/bwa" | ||
| export JAVA_INCLUDE="/System/Library/Frameworks/JavaVM.framework/Headers" | ||
| export TARGET_LIB="libbwa.dylib" | ||
| export EXTRA_LIBS="-lc -lz -lsupc++" | ||
| export LIBTOOL_COMMAND="libtool -dynamic" | ||
| make |
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