change

Former-commit-id: dab9662a50082e6ae76a8ec3391abb9b3295c0e9 [formerly 76e6c0c] [formerly e85355900940db170b5b0c5770372f402af9b189] [formerly ae7befcc01c68bcb87367cfe837281fea9f4a4e7 [formerly 3e5745879c0ded5db94d47bb908976aa55c916dc]] [formerly 8648bf4dabbe98db23bbf69e2e128fae2edeadbc [formerly 05da5ee]]
Former-commit-id: 7e7c3cc
Former-commit-id: 5618a1b8d8510d88d96aa548db608c31806cb644 [formerly 0f5da7a]
Former-commit-id: 3ae7ab3af1882cc013c256c185bcc8e9e2291b51
Former-commit-id: 5685054

CMakeLists.txt

@@ -31,6 +31,8 @@ add_executable(smashpp  src/main.cpp
                         )
 
 
+add_executable(smashpp-inv-rep src/invRep.cpp)
+
 #add_executable(excule_N src/excludeN.cpp)
 
 #add_executable(bench    src/bench.cpp)

bye

@@ -0,0 +1 @@
+NGAT

hi

@@ -0,0 +1 @@
+NGAT

mori

@@ -0,0 +1 @@
+AAAATGGGCGTACAATTAGACTGTGAATTCTAAGGAAATAAGTGCTAGTTGTATTGTCGGGAAGGACAACTGGGTACCCCTTAGTCACTCCTGAACTACGGAATGACGGAGCAGCATGATTACATCAGTGTTGACTGATATATAGTTAGATTTAGGTGTCGGCTAAATGTAGACTTTGGCGGAAAATCAATGCCTCGCTTCCACGCTTGTTGTAGTTCTACGGACTTACCGTTTGGTTAAAGAACATGTAAGTCGAGCGAGTTTTAGTTCCTCCGTTATTATAGGAGGTGCGTGCACCCAAATGCCAGCTCAGATAGAGGCCTGCACTTTGCTGGGTACCCAACCTGTGAAAACCCAAGCAGCAGGTCAGGCCACCCTCGGTTTAAGGAATTTTCCCAGTGCACTGCACATGAACTGAACCCAATACCAGAACGTTACATTTCACCTCTGGGTGTAATCATCTTTTAGGTTTAAATCCATCTGTGTGTAACTGTTAACTGATCGTTCAGTCTAGACTTCCGAGACCTCGTGCACCGCCTTGGGTTCACAAGCGGGCATTTGAATACTATCGCGCAACGGGGTGCCTGCCGTGATTACGCGCACCGCTTTTATGCTCGAGTTAAAGAAACCAACACTCATAAGTAGTTGACTAGATGCCAACTCGACGCGGTGGAGTAAATATCTTCGCAATGTTAGGTGAAAGCACCCATTGAATAAATTTCTTCGGTTCATTCATAGCGGTGTATCAACCCGGTAGCGAAGCCGTGAGGGACAAGCATGGGCGAGCGCATGACGCAAGGCGGGTTTCCGGTACTGCGCGGGGGGCTGTTTTGGGGGAGGGGTCGCCGTTGACCCGATCGAACACGTAAGAGCTAGTGGATGGTAGCCGACATGAAGATCTCTCGAACAACCCCTGACCCTGGCCGCGTACGTGAAAAAGGTCGCCCTGGAATCTCCGTGTGGAACAGGGTCTGATCCGTCGCGAACGGCATCAAGGCGC

refm.REMOVED.git-id

@@ -1 +1 @@
-30e3373f721b154dabe25e71f964ad974245dd55
+dea3db0aa7ff3e95ea470ef6fa89e6447aca9361

script/run.sh

@@ -15,60 +15,72 @@ fi
 
 ### Simulate synthetic dataset
 if [[ $SYNTHETIC -eq 1 ]]; then
-  ### Small sizes: ref:1000, tar:1000
-  ./goose-fastqsimulation -eh -eo -es -edb -rn 2 -ri 5 -ra 15 -rm 0 -s 101 \
-                          -ls 50 -n 5 -f 0.2,0.3,0.3,0.2,0.0                 r_a
-  ./goose-fastqsimulation -eh -eo -es -edb -rn 1 -ri 5 -ra 20 -rm 0 -s 68 \
-                          -ls 50 -n 5 -f 0.25,0.25,0.25,0.25,0.0             r_b
-  ./goose-fastqsimulation -eh -eo -es -edb -rn 3 -ri 5 -ra 10 -rm 0 -s 3 \
-                          -ls 50 -n 5 -f 0.25,0.25,0.25,0.25,0.0             r_c
-  ./goose-fastqsimulation -eh -eo -es -edb -rn 1 -ri 5 -ra 20 -rm 0 -s 1785 \
-                          -ls 50 -n 5 -f 0.3,0.2,0.2,0.3,0.0                 r_d
-  cat r_a r_b r_c r_d > refs
+  # ### Small sizes: ref:1000, tar:1000
+  # # ./goose-fastqsimulation -eh -eo -es -edb -rn 2 -ri 5 -ra 15 -rm 0 -s 101 \
+  # #                         -ls 50 -n 5 -f 0.2,0.3,0.3,0.2,0.0                 r_a
+  # # ./goose-fastqsimulation -eh -eo -es -edb -rn 1 -ri 5 -ra 20 -rm 0 -s 68 \
+  # #                         -ls 50 -n 5 -f 0.25,0.25,0.25,0.25,0.0             r_b
+  # # ./goose-fastqsimulation -eh -eo -es -edb -rn 3 -ri 5 -ra 10 -rm 0 -s 3 \
+  # #                         -ls 50 -n 5 -f 0.25,0.25,0.25,0.25,0.0             r_c
+  # # ./goose-fastqsimulation -eh -eo -es -edb -rn 1 -ri 5 -ra 20 -rm 0 -s 1785 \
+  # #                         -ls 50 -n 5 -f 0.3,0.2,0.2,0.3,0.0                 r_d
+  # ./goose-fastqsimulation -eh -eo -es -edb -rm 0 -s 201 -ls 50 -n 5 \
+  #                         -f 0.2,0.3,0.3,0.2,0.0                 r_a
+  # ./goose-fastqsimulation -eh -eo -es -edb -rm 0 -s 58 -ls 50 -n 5 \
+  #                         -f 0.25,0.25,0.25,0.25,0.0             r_b
+  # ./goose-fastqsimulation -eh -eo -es -edb -rm 0 -s 3 -ls 50 -n 5 \
+  #                         -f 0.25,0.25,0.25,0.25,0.0             r_c
+  # ./goose-fastqsimulation -eh -eo -es -edb -rm 0 -s 1785 -ls 50 -n 5 \
+  #                         -f 0.3,0.2,0.2,0.3,0.0                 r_d
+  # cat r_a r_b r_c r_d > refs
 
-  ./goose-mutatedna -mr 0.00 < r_d > t_a
-  ./goose-mutatedna -mr 0.01 < r_b > t_c
-  ./goose-mutatedna -mr 0.02 < r_a > t_b
-  ./goose-mutatedna -mr 0.05 < r_c > t_d
-  cat t_a t_b t_c t_d > tars
+  # cp r_a t_b
+  # cp r_b t_c
+  # cp r_c t_d
+  # cp r_d t_a
+  # # ./goose-mutatedna -mr 0.00 < r_d > t_a
+  # # ./goose-mutatedna -mr 0.01 < r_b > t_c
+  # # ./goose-mutatedna -mr 0.02 < r_a > t_b
+  # # ./goose-mutatedna -mr 0.05 < r_c > t_d
+  # cat t_a t_b t_c t_d > tars
 
   ### Medium sizes: ref:100000, tar:100000
-  ./goose-fastqsimulation -eh -eo -es -edb -rn 2 -ri 50 -ra 500 -rm 0 -s 1001 \
-                          -ls 100 -n 250 -f 0.25,0.25,0.25,0.25,0.0          r_a
-  ./goose-fastqsimulation -eh -eo -es -edb -rn 1 -ri 50 -ra 500 -rm 0 -s 608 \
-                          -ls 100 -n 250 -f 0.3,0.2,0.2,0.3,0.0              r_b
-  ./goose-fastqsimulation -eh -eo -es -edb -rn 3 -ri 50 -ra 500 -rm 0 -s 30 \
-                          -ls 100 -n 250 -f 0.2,0.3,0.3,0.2,0.0              r_c
-  ./goose-fastqsimulation -eh -eo -es -edb -rn 1 -ri 50 -ra 500 -rm 0 -s 17805 \
-                          -ls 100 -n 250 -f 0.25,0.25,0.25,0.25,0.0          r_d
+  ./goose-fastqsimulation -eh -eo -es -edb -rm 0 -s 1001 -ls 100 -n 250 \
+                          -f 0.25,0.25,0.25,0.25,0.0  r_a
+  ./goose-fastqsimulation -eh -eo -es -edb -rm 0 -s 608 -ls 100 -n 250 \
+                          -f 0.3,0.2,0.2,0.3,0.0      r_b
+  ./goose-fastqsimulation -eh -eo -es -edb -rm 0 -s 30 -ls 100 -n 250 \
+                          -f 0.2,0.3,0.3,0.2,0.0      r_c
+  ./goose-fastqsimulation -eh -eo -es -edb -rm 0 -s 17805 -ls 100 -n 250 \
+                          -f 0.25,0.25,0.25,0.25,0.0  r_d
   cat r_a r_b r_c r_d > refm
 
-  ./goose-mutatedna -mr 0.00 < r_d > t_a
+  ./goose-mutatedna -mr 0.00 < r_a > t_d
+  ./smashpp-inv-rep          < r_b > t_c
   ./goose-mutatedna -mr 0.01 < r_c > t_b
-  ./goose-mutatedna -mr 0.02 < r_b > t_c
-  ./goose-mutatedna -mr 0.05 < r_a > t_d
+  ./goose-mutatedna -mr 0.00 < r_d > t_a
   cat t_a t_b t_c t_d > tarm
 
-  ### Large sizes: ref:5000000, tar:5000000
-  ./goose-fastqsimulation -eh -eo -es -edb -rn 2 -ri 500 -ra 1000 -rm 0 \
-                          -ls 100 -n 12500 -f 0.3,0.2,0.3,0.2,0.0 -s 10101   r_a
-  ./goose-fastqsimulation -eh -eo -es -edb -rn 1 -ri 500 -ra 1000 -rm 0 \
-                          -ls 100 -n 12500 -f 0.3,0.2,0.2,0.3,0.0 -s 6018    r_b
-  ./goose-fastqsimulation -eh -eo -es -edb -rn 3 -ri 500 -ra 1000 -rm 0 \
-                          -ls 100 -n 12500 -f 0.25,0.25,0.25,0.25,0.0 -s 10  r_c
-  ./goose-fastqsimulation -eh -eo -es -edb -rn 1 -ri 500 -ra 1000 -rm 0 \
-                          -ls 100 -n 12500 -f 0.25,0.25,0.25,0.25,0.0 -s 7   r_d
-  cat r_a r_b r_c r_d > refl
+  # ### Large sizes: ref:5000000, tar:5000000
+  # ./goose-fastqsimulation -eh -eo -es -edb -rn 2 -ri 500 -ra 1000 -rm 0 \
+  #                         -ls 100 -n 12500 -f 0.3,0.2,0.3,0.2,0.0 -s 10101   r_a
+  # ./goose-fastqsimulation -eh -eo -es -edb -rn 1 -ri 500 -ra 1000 -rm 0 \
+  #                         -ls 100 -n 12500 -f 0.3,0.2,0.2,0.3,0.0 -s 6018    r_b
+  # ./goose-fastqsimulation -eh -eo -es -edb -rn 3 -ri 500 -ra 1000 -rm 0 \
+  #                         -ls 100 -n 12500 -f 0.25,0.25,0.25,0.25,0.0 -s 10  r_c
+  # ./goose-fastqsimulation -eh -eo -es -edb -rn 1 -ri 500 -ra 1000 -rm 0 \
+  #                         -ls 100 -n 12500 -f 0.25,0.25,0.25,0.25,0.0 -s 7   r_d
+  # cat r_a r_b r_c r_d > refl
 
-  ./goose-mutatedna -mr 0.00 < r_c > t_a
-  ./goose-mutatedna -mr 0.01 < r_b > t_b
-  ./goose-mutatedna -mr 0.02 < r_a > t_c
-  ./goose-mutatedna -mr 0.05 < r_d > t_d
-  cat t_a t_b t_c t_d > tarl
+  # ./goose-mutatedna -mr 0.00 < r_c > t_a
+  # ./goose-mutatedna -mr 0.01 < r_b > t_b
+  # ./goose-mutatedna -mr 0.02 < r_a > t_c
+  # ./goose-mutatedna -mr 0.05 < r_d > t_d
+  # cat t_a t_b t_c t_d > tarl
 
   rm r_* t_*
 fi
 
 ### Get real dataset
 #if [[ $REAL -eq 1 ]]; then
-#fi
+#fi

smashpp.REMOVED.git-id

@@ -1 +1 @@
-8e1251bf63b02eee2bfc1ff20993845a5f985318
+60f94b22879cfff5a2a3e71ed9d4078a923567b7

src/filter.cpp

@@ -481,6 +481,22 @@ void Filter::aggregate_final_pos (const string& ref, const string& tar) const {
     midf0.close();  remove(midf0Name.c_str());
     finf.close();
   }
+  else if (midf0IsEmpty && !midf1IsEmpty) {
+    ifstream midf1(midf1Name);
+    ofstream finf(gen_name(ref, tar, Format::POSITION));
+
+    finf << POS_HDR <<'\t'<< file_name(ref) <<'\t'<< to_string(file_size(ref))
+                    <<'\t'<< file_name(tar) <<'\t'<< to_string(file_size(tar));
+    finf << '\n';
+
+    const u64 size = file_size(midf1Name);
+    vector<char> buffer(size, 0);
+    midf1.read (buffer.data(), size);
+    finf.write(buffer.data(), size);
+
+    midf1.close();  remove(midf1Name.c_str());
+    finf.close();
+  }
   else {
     ifstream midf0(midf0Name), midf1(midf1Name);
     ofstream finf(gen_name(ref, tar, Format::POSITION));

src/invRep.cpp

@@ -0,0 +1,48 @@
+#include <iostream>
+#include <fstream>
+#include <vector>
+#include <algorithm>
+using namespace std;
+
+// a,A->84(T)  c,C->71(G)  g,G->67(C)  t,T->65(A)  n,N->78(N)
+static constexpr char REV[123] {
+ 0, 0, 0,  0,  0,  0, 0,  0, 0, 0,  0,  0, 0, 0, 0, 0,  0,  0,  0,  0,   // #20
+ 0, 0, 0,  0,  0,  0, 0,  0, 0, 0,  0,  0, 0, 0, 0, 0,  0,  0,  0,  0,
+ 0, 0, 0,  0,  0,  0, 0,  0, 0, 0,  0,  0, 0, 0, 0, 0,  0,  0,  0,  0,
+ 0, 0, 0,  0,  0,'T', 0,'G', 0, 0,  0,'C', 0, 0, 0, 0,  0,  0,'N',  0,
+ 0, 0, 0,  0,'A',  0, 0,  0, 0, 0,  0,  0, 0, 0, 0, 0,  0,'T',  0,'G',
+ 0, 0, 0,'C',  0,  0, 0,  0, 0, 0,'N',  0, 0, 0, 0, 0,'A',  0,  0,  0,
+ 0, 0, 0
+};
+
+int main (int argc, char* argv[]) {
+  const string inFileName = argv[1];
+  const string outFileName = argv[2];
+  size_t size;
+  {
+  ifstream inFile(inFileName, ifstream::ate | ifstream::binary);
+  size = inFile.tellg();
+  inFile.close();
+  }
+
+  ifstream inFile(inFileName);
+  vector<char> buffer(size, 0);
+  inFile.read(buffer.data(), size);
+  inFile.close();
+
+  // reverse(buffer.begin(), buffer.end());
+
+  // // for (auto& c : buffer)
+  // //   c = REV[static_cast<unsigned char>(c)];
+
+  //   for (auto it=buffer.data();it<buffer.data()+size;++it)
+  //     *it = REV[static_cast<unsigned char>(*it)];
+
+
+
+  ofstream outFile(outFileName);
+  outFile.write(buffer.data(), size);
+  outFile.close();
+
+  return 0;
+}

tars

@@ -1 +1 @@
-CATGTTCTTTAACCAAACGGTAAGTCCGTAGAACTACAACAAGCGTGGAAGCGAGGCATTGATTTTCCGCCAAAGTCTACATTTAGCCGACACCTAAATTTAACTATATATCAGTCAACACTGATGTAATCATGCTGCTCCGTCATTCAATAGTTCAGGAGTGACTAAGGGGTACCCAGTTGTCCTTCCCGACAATACATCTAGCACTTATTTCCTACACCTAAATTTAACATTGTACGCCCATTTTTCTTATTTGATGACGCATCGTAAGGACCAGGCGTCGGAGCAGCCAAGCTTTTAGAACACGAGCGGTAGTCCGACCTGCGGGGGCCGGGTTCTGGCCGGTGTACTTCGGTTCTCGGGTGAGCAGGCCCAGCAGCCCCAGCACGCTCTGAACGAAGGCAGTCCCAGCTCGCTTACCATGTCCGAACGACCACAAAGGGACGCAGCACGTGGGTGTTACGTGCTCAAGGTGGGGCCTGTGGGACCGACTGTGACGGAGAGATCCTATCATTAGGAGGAGTTGTCTTCTCGGCGTTCATTAGTCCCCAGGAAGGATTAGACTGATACTGGGTCTCCGCGCATGGCGCCTTCATAAGAAAACGTTTAAGAGCAGTCTAGGCCCATAATAATAGGAGGCGAGACGGAACCGCTCTCCACAGAAGAACATTACGGGGCTTAAGCTTGCCTGCCGGATGCTAGTAACAAACAGGAACGTGAACTTACATGCGTAGTCTTCACGTTGACATGACAGTTACACACAGATGGAATTAAGCCTAAAAGATGATTACACCGGCAACTGAAATGTTACGTTCTGGTATTGGGTTCATTTCATGTGCAGTGCGACCGCAAAATTCCTTAAACCGAGGGTGGCCTGACCTGCTGCTTGGGTTTAACCGAGTTGGGGACCTAGTAAAGTGCAGGCCTCTATCTGAGTTGGCGCAGGCGTAACGCACCTCCTATAATAACGGAGCAACTAAAACTCGGGTTCAGTTTGTAC
+TACATGTTCTTTAACCAAACGGTAAGTCCGTAGAACTACAACAAGCGTGGAAGCGAGGCATTGATTTTCCGCCAAAGTCTACATTTAGCCGACACCTAAATCTAACTATATATCAGTCAACACTGATGTAATCATGCTGCTCCGTCATTCCGTAGTTCAGGAGTGACTAAGGGGTACCCAGTTGTCCTTCCCGACAATACAACTAGCACTTATTTCCTTAGAATTCACAGTCTAATTGTACGCCCATTTTGCGCCTTGATGCCGTTCGCGACGGATCAGACCCTGTTCCACACGGAGATTCCAGGGCGACCTTTTTCACGTACGCGGCCAGGGTCAGGGGTTGTTCGAGAGATCTTCATGTCGGCTACCATCCACTAGCTCTTACGTGTTCGATCGGGTCAACGGCGACCCCTCCCCCAAAACAGCCCCCCGCGCAGTACCGGAAACCCGCCTTGCGTCATGCGCTCGCCCATGCTTGTCCCTCACGGCTTCGCTACCGGGTTGATACACCGCTATGAATGAACCGAAGAAATTTATTCAATGGGTGCTTTCACCTAACATTGCGAAGATATTTACTCCACCGCGTCGAGTTGGCATCTAGTCAACTACTTATGAGTGTTGGTTTCTTTAACTCGAGCATAAAAGCGGTGCGCGTAATCACGGCAGGCACCCCGTTGCGCGATAGTATTCAAATGCCCGCTTGTGAACCCAAGGCGGTGCACGAGGTCTCGGAAGTCTAGACTGAACGATCAGTTAACAGTTACACACAGATGGATTTAAACCTAAAAGATGATTACACCCAGAGGTGAAATGTAACGTTCTGGTATTGGGTTCAGTTCATGTGCAGTGCACTGGGAAAATTCCTTAAACCGAGGGTGGCCTGACCTGCTGCTTGGGTTTTCACAGGTTGGGTACCCAGCAAAGTGCAGGCCTCTATCTGAGCTGGCATTTGGGTGCACGCACCTCCTATAATAACGGAGGAACTAAAACTCGCTCGACT