Coverage filter

.gitignore

@@ -1,14 +1,7 @@
 ococo
-*.html
 
-.vscode/.*
-*~
-*.swp
-*.anjuta
-.anjuta*
-
-CTestTestfile.cmake
-Testing
+# Prerequisites
+*.d
 
 # Compiled Object files
 *.slo
@@ -27,6 +20,7 @@ Testing
 
 # Fortran module files
 *.mod
+*.smod
 
 # Compiled Static libraries
 *.lai
@@ -38,3 +32,56 @@ Testing
 *.exe
 *.out
 *.app
+
+# Prerequisites
+*.d
+
+# Object files
+*.o
+*.ko
+*.obj
+*.elf
+
+# Linker output
+*.ilk
+*.map
+*.exp
+
+# Precompiled Headers
+*.gch
+*.pch
+
+# Libraries
+*.lib
+*.a
+*.la
+*.lo
+
+# Shared objects (inc. Windows DLLs)
+*.dll
+*.so
+*.so.*
+*.dylib
+
+# Executables
+*.exe
+*.out
+*.app
+*.i*86
+*.x86_64
+*.hex
+
+# Debug files
+*.dSYM/
+*.su
+*.idb
+*.pdb
+
+# Kernel Module Compile Results
+*.mod*
+*.cmd
+.tmp_versions/
+modules.order
+Module.symvers
+Mkfile.old
+dkms.conf

.vscode/c_cpp_properties.json

@@ -2,32 +2,48 @@
     "configurations": [
         {
             "name": "Mac",
-            "includePath": ["/usr/include"],
-            "browse" : {
-                "limitSymbolsToIncludedHeaders" : true,
-                "databaseFilename" : ""
-            }
+            "includePath": [
+                "/usr/include",
+                "/usr/local/Cellar/gcc/8.2.0/include/c++/8.2.0",
+                "${workspaceFolder}/ext/htslib"
+            ],
+            "browse": {
+                "limitSymbolsToIncludedHeaders": true,
+                "databaseFilename": ""
+            },
+            "macFrameworkPath": [
+                "/System/Library/Frameworks",
+                "/Library/Frameworks"
+            ],
+            "intelliSenseMode": "clang-x64"
         },
         {
             "name": "Linux",
-            "includePath": ["/usr/include"],
-            "browse" : {
-                "limitSymbolsToIncludedHeaders" : true,
-                "databaseFilename" : ""
-            }
+            "includePath": [
+                "/usr/include"
+            ],
+            "browse": {
+                "limitSymbolsToIncludedHeaders": true,
+                "databaseFilename": ""
+            },
+            "intelliSenseMode": "gcc-x64"
         },
         {
             "name": "Win32",
-            "includePath": ["c:/Program Files (x86)/Microsoft Visual Studio 14.0/VC/include"],
-            "browse" : {
-                "limitSymbolsToIncludedHeaders" : true,
-                "databaseFilename" : ""
-            }
+            "includePath": [
+                "c:/Program Files (x86)/Microsoft Visual Studio 14.0/VC/include"
+            ],
+            "browse": {
+                "limitSymbolsToIncludedHeaders": true,
+                "databaseFilename": ""
+            },
+            "intelliSenseMode": "msvc-x64"
         }
     ],
-    "clang_format" : {
-        "style" : "file",
-        "fallback-style" : "LLVM",
-        "sort-includes" : false
-    }
-}
+    "clang_format": {
+        "style": "file",
+        "fallback-style": "LLVM",
+        "sort-includes": false
+    },
+    "version": 4
+}

.vscode/settings.json

@@ -1,4 +1,40 @@
 // Place your settings in this file to overwrite default and user settings.
 {
-	"editor.tabSize": 4
+	"editor.tabSize": 4,
+	"files.associations": {
+		"ios": "cpp",
+		"*.tcc": "cpp",
+		"cctype": "cpp",
+		"clocale": "cpp",
+		"cmath": "cpp",
+		"cstdarg": "cpp",
+		"cstddef": "cpp",
+		"cstdio": "cpp",
+		"cstdlib": "cpp",
+		"cstring": "cpp",
+		"ctime": "cpp",
+		"cwchar": "cpp",
+		"cwctype": "cpp",
+		"exception": "cpp",
+		"iomanip": "cpp",
+		"iosfwd": "cpp",
+		"iostream": "cpp",
+		"istream": "cpp",
+		"limits": "cpp",
+		"memory": "cpp",
+		"ostream": "cpp",
+		"sstream": "cpp",
+		"stdexcept": "cpp",
+		"streambuf": "cpp",
+		"array": "cpp",
+		"cinttypes": "cpp",
+		"cstdint": "cpp",
+		"type_traits": "cpp",
+		"typeinfo": "cpp",
+		"string": "cpp",
+		"__nullptr": "cpp",
+		"system_error": "cpp",
+		"chrono": "cpp"
+	},
+	"C_Cpp.intelliSenseEngineFallback": "Enabled"
 }

LICENSE

@@ -1,6 +1,6 @@
 The MIT License (MIT)
 
-Copyright (c) 2016-2017 Karel Brinda ([email protected])
+Copyright (c) 2016-2019 Karel Brinda ([email protected])
 
 Permission is hereby granted, free of charge, to any person obtaining a copy
 of this software and associated documentation files (the "Software"), to deal
@@ -19,4 +19,3 @@ AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
 LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
 OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
 SOFTWARE.
-

Makefile

@@ -1,5 +1,9 @@
 CXX      ?= g++
-CXXFLAGS  = -std=c++11 -Wall -Wextra -Wno-missing-field-initializers -g -O2
+CXXFLAGS  = -std=c++11 -Wall -Wpedantic -Wextra -g -O3 \
+
+#-Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wold-style-cast -Wuseless-cast \
+#-Wdouble-promotion -Wshadow
+
 LIBS      = -lm -lz -lpthread
 
 PREFIX    = $(DESTDIR)/usr/local
@@ -12,12 +16,16 @@ HTSLIB    = $(HTSLIBDIR)/libhts.a
 HTSLIBINCLUDE = $(HTSLIBDIR)
 HTSLIB_VERSION = b6aa0e6
 
-ofiles    = src/main.cpp.o src/misc.cpp.o src/params.cpp.o
+ofiles    = src/main.cpp.o
 hfiles    = $(wildcard src/*.h)
 
-.PHONY: all clean install ococo readme
+.PHONY: all clean cleanall install readme format test big
+
+.SUFFIXES:
 
-all: ococo
+.SECONDARY:
+
+all: ococo $(ofiles)
 
 install: ococo
 	install  ococo $(BINDIR)/ococo
@@ -49,8 +57,19 @@ readme:
 	  > README.md
 	markdown_py README.md > README.html
 
+format:
+	clang-format -i src/*.cpp src/*.h
+
 clean:
-	$(MAKE) -C ext/htslib clean
+	$(MAKE) -C tests clean
 	rm -f src/*.o
 	rm -f ococo
 
+cleanall: clean
+	$(MAKE) -C ext/htslib clean
+
+test: ococo
+	$(MAKE) -C tests
+
+big:
+	(samtools view -H ./test.bam ; for i in $$(seq 100); do samtools view test.bam; done) | samtools view -b > big.bam

ococo.1

@@ -31,6 +31,12 @@ Print inferred variants in VCF (\- for standard output).
 \fB\-P\fR, \fB\-\-pileup\fR FILE
 Print SAMtools pileup (\- for standard output).
 .TP
+\fB\-O\fR, \fB\-\-output\fR FILE
+Output SAM/BAM file for filtered alignments (- for standard output).
+.TP
+\fB\-C\fR, \fB\-\-cov\-filt\fR INT
+Filter alignments when coverage is greater than INT [-1].
+.TP
 \fB\-\-verbose\fR
 Use the verbose mode (report every update of a counter).
 .SS "Parameters for consensus calling:"
@@ -39,9 +45,10 @@ Use the verbose mode (report every update of a counter).
 Counter configuration [ococo32].
 
 .TS
-l	l	l	.
+l	|	l	|	l	.
 .B
 configuration	bits/counter	bits/position
+_
 ococo16	3	16
 ococo32	7	32
 ococo64	15	64
@@ -51,10 +58,11 @@ ococo64	15	64
 \fB\-m\fR, \fB\-\-mode\fR STR
 Mode [batch].
 
-.TS
-l	l	.
+.TS 
+l	|	l	.
 .B
 mode	description
+_
 real\-time	updates reported immediately
 batch	updates reported after end of algn stream
 .TE