improved user interface

CMakeLists.txt

@@ -43,7 +43,7 @@ add_executable(proali
         src/util/nucleotideCodeSubstitutionMatrix.h
         src/util/parameters.cpp
         src/util/parameters.h
-        song.cpp
+        main.cpp
         src/model/Fasta.cpp
         src/model/Fasta.h
         src/model/variant.cpp
@@ -54,18 +54,9 @@ add_executable(proali
         src/model/Gene.h
         src/model/Matrix.cpp
         src/model/Matrix.h
-        src/model/MsaWindow.cpp
-        src/model/MsaWindow.h
-        src/model/MsaSingleRecord.cpp
-        src/model/MsaSingleRecord.h
-        src/model/MsaFileRecord.cpp
-        src/model/MsaFileRecord.h
-        src/model/TwoSeqOfMsaResult.cpp
-        src/model/TwoSeqOfMsaResult.h
         src/model/FirstLastList.cpp
         src/model/FirstLastList.h
         src/model/STRAND.h
-        src/model/REGION.h
         src/model/Seed.h
         src/model/Seed.cpp
         src/model/PairedSimilarFragment.cpp
@@ -80,25 +71,17 @@ add_executable(proali
         src/impl/checkOrfState.cpp
         src/impl/checkOrfState.h
         src/util/util.h
-        src/impl/nA2AA.cpp
-        src/impl/nA2AA.h
         src/impl/getSubsequence.cpp
         src/impl/getSubsequence.h
         src/impl/readGffFile.cpp
         src/impl/readGffFile.h
-        src/impl/coordinateLiftOver.cpp
-        src/impl/coordinateLiftOver.h
         src/impl/getSequencesFromGff.cpp
         src/impl/getSequencesFromGff.h
         src/service/service.h
         src/myImportandFunction/myImportantFunction.h
         src/impl/TranscriptUpdateInformation.cpp
         src/impl/TranscriptUpdateInformation.h
-        src/impl/FileWriteCatch.cpp
-        src/impl/FileWriteCatch.h
         src/tests/util/nucleotideCodeSubstitutionMatrix_test.cpp
-        src/model/Range.cpp src/model/Range.h src/model/AlignmentMatch.cpp
-        src/model/AlignmentMatch.h
         src/service/TransferGffWithNucmerResult.cpp
         src/service/TransferGffWithNucmerResult.h
         src/myImportandFunction/alignSlidingWindow.cpp
@@ -111,8 +94,8 @@ add_executable(proali
         src/tests/impl/readFastaFile_test.cpp
         src/impl/deNovoGenomeVariantCalling.cpp
         src/impl/deNovoGenomeVariantCalling.h
-        src/model/OrthologPair.cpp
-        src/model/OrthologPair.h
+        src/model/AlignmentMatch.cpp
+        src/model/AlignmentMatch.h
         src/model/Score.cpp
         src/model/Score.h
         src/impl/geneSyntenic.cpp

README.md

@@ -41,11 +41,12 @@ minimap2 -ax splice -t 90 -a -uf -p 0.4 -C5 Sorghum_bicolor.Sorghum_bicolor_NCBI
 proali proali -i Zea_mays.AGPv4.34.gff3 -r Zea_mays.AGPv4.dna.toplevel.fa -a cds.sam -s Sorghum_bicolor.Sorghum_bicolor_NCBIv3.dna.toplevel.fa -w 20000 -R 1 -Q 2 -O 0 -D 32 -o alignment -f
 ```
 
-### Variant calling for different accessions
-This module perform base pair resolution genome alignment for two genomes. A query chromosome sequence would be aligned against the reference chromosome with the same name end-to-end. \
+### genome alignment without rearrangement
+This module perform base pair resolution sequence alignment for two genomes. A query chromosome sequence would be aligned against the reference chromosome with the same name end-to-end. \
+Inversions \
 The output could be end-to-end sequence alignment for the whole chromosome in maf format. \
 Or alignment for each anchor region and inter anchor region with length shorter than the sequence alignment window width. \
-A variant calling result in vcf format also would be created which is derived from end-to-end alignment. \
+A variant calling result in vcf format could be created which is derived from end-to-end alignment. \
 \
 data: Arabidopsis thaliana Col-o reference genome and GFF3 annotation file from https://www.arabidopsis.org/\
 Arabidopsis thaliana Ler-0 accession assembly from http://www.pnas.org/content/113/28/E4052

main.cpp

@@ -1,8 +1,62 @@
+/*
+ * =====================================================================================
+ *
+ *       Filename:  song.cpp
+ *
+ *    Description:  
+ *
+ *        Version:  1.0
+ *        Created:  06/23/2017 21:51:57
+ *       Revision:  none
+ *       Compiler:  gcc
+ *
+ *         Author:  Baoxing Song (songbx.me), [email protected]
+ *
+ * =====================================================================================
+ */
+#include <stdlib.h>
+/*************************************************************************
+
+
+
+
+ ************************************************************************/
+
+#include "src/controlLayer.h"
 #include "./googletest/googletest/include/gtest/gtest.h"
+using namespace std;
 
 
-int main(int argc, char ** argv) {
-    testing::InitGoogleTest(&argc, argv);
-    RUN_ALL_TESTS();
+int main(int argc, char** argv){
+//testing::InitGoogleTest(&argc, argv);
+//RUN_ALL_TESTS();
+//return 0;
+    if( argc<=1 ){
+        usage();
+        return 1;
+    }
+    std::string program = argv[1];
+    if( program.compare("-h") == 0 || program.compare("--help") == 0 ){
+        usage();
+        exit(1);
+    }
+    InputParser inputParser (argc, argv);
+    string parameterFile;
+    std::string exepath = getexepath(argv);
+    if( inputParser.cmdOptionExists("-parameter")){
+        parameterFile = inputParser.getCmdOption("-parameter");
+    }else{
+        parameterFile = exepath + "/configure";
+    }
+    std::map<std::string, std::string> parameters = initialize_paramters(parameterFile, exepath);
+    if( program.compare("gff2seq") == 0 ) {
+        return gff2seq(--argc, ++argv, parameters);
+    } else if ( program.compare("proali") == 0 ) {
+        return proportationalAlignment(--argc, ++argv, parameters);
+    } else if ( program.compare("genoAli") == 0 ) {
+        return genomeAlignment(--argc, ++argv, parameters);
+    } else{
+        usage();
+    }
     return 0;
 }