Issue 180

algbio · Jan 14, 2022 · a68b0c9 · a68b0c9
1 parent 2fabec7
commit a68b0c9
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Showing 4 changed files with 21 additions and 6 deletions.
diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml
@@ -16,14 +16,16 @@ jobs:
     name: Linux test (remote)
     runs-on: ubuntu-latest
     env: 
-      EXE: ./bin/kmc      
-      KMC_SINGLE_READ: ./tests/kmc_CLI/data/single_read.fq      
-
+      EXE: ./bin/kmc
+      EXE_DUMP: ./bin/kmc_dump
+      KMC_SINGLE_READ: ./tests/kmc_CLI/data/single_read.fq
+      DATA_DIR: ./tests/kmc_CLI/data/
     steps:
     - uses: actions/checkout@v2
     - name: make
-      run: make -j12 kmc
-
+      run: |
+        g++ -v
+        make -j12 kmc kmc_tools kmc_dump
 
     - name: KMC single read, k=28, ci=1
       run: |
@@ -38,6 +40,11 @@ jobs:
       run: |
         $EXE -k10 -v  $KMC_SINGLE_READ 10mers .
         $EXE -k9 -v -fkmc 10mers 9mers .
+    - name: issue 180
+      run: |
+        $EXE -v -k5 -fa -ci1 -t1 $DATA_DIR/issue-180/input.fa bug-report.kmc .
+        $EXE_DUMP bug-report.kmc issue-180.kmers
+        cmp issue-180.kmers $DATA_DIR/issue-180/pattern.dump
         
   macos-remote:
     name: macOS build (remote)

diff --git a/kmc_api/kmc_file.h b/kmc_api/kmc_file.h
@@ -43,8 +43,8 @@ class CKMCFile
 		uint64_t leftToRead{};
 		uint64 prefixMask; //for kmc2 db
 		FILE* file;
-		uint64_t totalKmers; //for
 		bool isKMC1 = false;
+		uint64_t totalKmers; //for
 
 		void reload()
 		{

diff --git a/tests/kmc_CLI/data/issue-180/input.fa b/tests/kmc_CLI/data/issue-180/input.fa
@@ -0,0 +1,2 @@
+>palindrome
+AACTGACATGTCAGTT
diff --git a/tests/kmc_CLI/data/issue-180/pattern.dump b/tests/kmc_CLI/data/issue-180/pattern.dump
@@ -0,0 +1,6 @@
+AACTG	2
+ACATG	2
+ACTGA	2
+ATGTC	2
+CTGAC	2
+TGACA	2
-Original file line number
+Diff line change
@@ -0,0 +1,6 @@
+    AACTG	2
+    ACATG	2
+    ACTGA	2
+    ATGTC	2
+    CTGAC	2
+    TGACA	2