code

BamDeal.cpp

@@ -0,0 +1,79 @@
+#include <iostream>
+#include <fstream>
+#include <sstream>
+#include <string>
+#include <cstdlib>
+#include <stdio.h>
+#include <string.h>
+#include <zlib.h>
+#include "src/convert/covert.h"
+#include "src/modify/modify.h"
+#include "src/statistics/statistics.h"
+#include "src/visualize/visualize.h"
+
+using namespace std;
+
+int convert_main(int argc, char *argv[]) ;
+int modify_main(int argc, char *argv[]);
+int statistics_main(int argc, char *argv[]);
+int visualize_main(int argc, char *argv[]);
+
+static int  AllTools_usage ()
+{
+	cerr <<"Program: BamDeal\nVersion: 0.27\thewm2008@gmail.com\t"<<__DATE__<<endl;
+
+	cerr<<""
+		"\n"
+		"\tUsage:\n\n"
+		"\t\tconvert        convert tools\n"
+		"\t\tmodify         modify tools\n"
+		"\t\tstatistics     statistics analysis tools\n"
+		"\t\tvisualize      visualize tools for bam\n"
+		"\n"
+		"\t\tHelp           Show help in detail\n"
+		"\n";
+	return 1;
+}
+
+static int  AllTools_usage2 ()
+{
+	cerr <<"Program: BamDeal\nVersion: 0.27\thewm2008@gmail.com\t"<<__DATE__<<endl;
+
+	cerr<<""
+		"\n"
+		"\tUsage:\n\n"
+		"\t\tconvert        convert tools\n"
+		"\t\tmodify         modify tools\n"
+		"\t\tstatistics     statistics analysis tools\n"
+		"\t\tvisualize      visualize tools for bam\n"
+		"\n"
+		"\t\tHelp           Show help in detail\n"
+		"\n"
+		"\t\t✉️ hewm2008@gmail.com / hewm2008@qq.com\n"
+		"\t\tjoin the QQ Group : 12529366\n"
+		"\n";
+	return 1;
+}
+
+
+int main(int argc, char *argv[])
+{
+	if (argc < 2) { return AllTools_usage(); }
+	else if (strcmp(argv[1], "convert") == 0) { return convert_main(argc-1, argv+1) ; }
+	else if (strcmp(argv[1], "statistics") == 0) { return statistics_main(argc-1, argv+1) ; }
+	else if (strcmp(argv[1], "visualize") == 0) { return visualize_main(argc-1, argv+1) ; }
+	else if (strcmp(argv[1], "modify") == 0) { return modify_main(argc-1, argv+1) ; }
+	else if (strcmp(argv[1], "Help") == 0 || strcmp(argv[1], "help") == 0 || strcmp(argv[1], "?")== 0 || ( argv[1][0] == '-' &&( argv[1][1] =='h' || argv[1][1] =='H' || argv[1][1] =='?' ) )  || strcmp(argv[1], "less") == 0 )
+	{
+		return  AllTools_usage2();
+	}
+	else
+	{
+		cerr<<"BamDeal [main] unrecognized command "<<argv[1]<<endl;
+		return 1;
+	}
+
+	return 0;
+}
+
+

Install.Readme

@@ -0,0 +1,34 @@
+
+make sure:
+   a.   libhts / htslib (>=1.12) had done ( http://www.htslib.org/download/)
+   b.   gcc/g++  ver  >= 4.8  // support Flag [ --std=c++11 ]
+
+#############################
+Only two step :
+
+1  ./configure
+   #  you can usr the  usr the  LDFLAGS  to find the htslib library and CXXFLAGS and CFLAGS to find the htslib header
+   #  ./configure LDFLAGS=-L/usr/lib/  CFLAGS="-I/usr/include/"  CXXFLAGS="-I/usr/include/"
+   #  Export LIBRARY/CFLAGS/CXXFLAGS environment variables to set the htslib path also can be a way to compile, such : export LD_LIBRARY_PATH=/usr/lib:$LD_LIBRARY_PATH
+
+2   make
+
+
+Note if it can't work . follow below  B1-B6  or use the  static Compiled [BamDeal_Linux ] 
+
+############################################
+ #autoscan ./
+ #cp configure.scan configure.ac
+
+# if can't work,  follow below 6  commands
+B1:     aclocal             #//   src/automake-1.9/aclocal
+B2:     autoconf            #//   src/automake-1.9/autoconf
+B3:     autoheader          #//   src/automake-1.9/autoheader 
+B4:     automake --add-missing   #//  src/automake-1.9/automake  --add-missing 
+B5:      ./configure     
+B6:      make 
+#############################################
+#swimming in the sky & flying in the sea#
+
+
+

LICENSE

@@ -19,3 +19,4 @@ 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.
+