code

INSTALL.txt

@@ -0,0 +1,69 @@
+fqcheck : fqcheck 
+
+1)  Introduction
+------------
+
+This software relies on two other library packages [zlib and gzstream]
+g++ > 4.9  is bester
+
+----------------------  zlib   infomation ----------------------------
+If  Lib [zlib] do not work
+you can download form this website and install it
+http://www.zlib.net/
+
+----------------------  gzstream  infomation ----------------------------
+If  Lib [gzstream] do not work
+you can download form this website and install it
+http://www.cs.unc.edu/Research/compgeom/gzstream/
+
+
+
+2) linux/Unix INSTALL
+--------------------------------------
+
+Just execute as follows :
+                         tar -zxvf  fqcheckXXX.tar.gz
+                         cd fqcheckXXX.tar.gz;
+                         make ; make clean
+                         ./bin/fqcheck
+
+#I had compiled and installed these two library packages [zlib and gzstream] on the linux X64 platform
+if Link do not work ,try Re-install these two  librarys and copy them to the  library Dir
+
+                     fqcheck-xx/include
+                     fqcheck-xx/lib
+
+
+
+3)  macOS  platform INSTALL
+
+you should  must  two  library [zlib and gzstream] and copy them to the corresponding library directory
+
+
+#step1 :Should must <b>re-install</b>  two  library [zlib and gzstream]
+                    see  [zlib and gzstream] website
+
+#step2  :  # Copy these two library into the corresponding library directory
+
+                    cp libz.a libz.so*      fqcheck-xx/lib
+                    cp libgzstream.a        fqcheck-xx/lib
+
+
+#step3  :
+
+sh make.sh # or [make && make clean]
+
+# if software can not find the htslib Path ,you can vim the make.sh  or  Makefile [-I -L]
+
+
+4) Contact
+email: [email protected] / [email protected]
+join the QQ Group : 125293663
+
+
+
+######################swimming in the sky and flying in the sea ########################### ##
+
+
+
+

Makefile

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+CXX=g++
+BIN := ./bin
+
+LDFLAGS=-lz
+INCLUDE=-I./include
+LIBS=-L./lib
+
+CXXFLAGS= -g  -O3  $(INCLUDE) $(LIBS)
+#  you can add the [ -I /path/.../samtools-1.6/htslib-1.6   -L /path/.../samtools-1.6/htslib-1.6 ] here #no need by fqcheck
+
+
+all: $(BIN)/fqcheck
+
+$(BIN)/fqcheck: $(BIN)/../src/fqcheck.o 
+	$(CXX)   $^ -o $@   $(LDFLAGS)  $(INCLUDE) $(LIBS)
+
+$(BIN)/%.o: %.cpp
+	$(CXX)  -c $(CXXFLAGS)  $< -o $@ 
+
+clean:
+	$(RM) $(BIN)/*.o  $(BIN)/../src/*.o
+

README.md

@@ -63,9 +63,9 @@ Usage:fqcheck  -InFq1 <in.fq>  -OutStat1 <out.fqcheck>  [options]
 some stat file will ouput.  
 Also if the system has <b> gnuplot</b> and <b> convert</b> commands installed, the following pictures will be output
 
-![base.png](https://github.com/hewm2008/fqcheck/blob/main/Example/base.png)
+![base.png](https://github.com/hewm2008/fqcheck/blob/main/example/base.png)
 
-![qual.png](https://github.com/hewm2008/fqcheck/blob/main/Example/qual.png)
+![qual.png](https://github.com/hewm2008/fqcheck/blob/main/example/qual.png)
 
 ###  4) Discussing
 ------------

SourceMe2.sh

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+prefix=/zfssz5/BC_PUB/Software/01.Usr  # may the  Gzstream  zlib install  path
+export PATH=/ifswh2/SOLEXA/hdp4000/bin:/zfssz5/BC_PUB/Software/03.Soft_ALL/gnuplot-5.2/bin/:$prefix/bin:$PATH  # may gnuplot here
+export LD_LIBRARY_PATH=$prefix/lib:$prefix/lib64:$LD_LIBRARY_PATH  

bin/SourceMe2.sh

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+prefix=/zfssz5/BC_PUB/Software/01.Usr  # may the  Gzstream  zlib install  path
+export PATH=/ifswh2/SOLEXA/hdp4000/bin:/zfssz5/BC_PUB/Software/03.Soft_ALL/gnuplot-5.2/bin/:$prefix/bin:$PATH  # may gnuplot here
+export LD_LIBRARY_PATH=$prefix/lib:$prefix/lib64:$LD_LIBRARY_PATH  

example/1.adapter.stat

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+adapter_id	polluted_reads	empty_reads	adapter_sequence
+iPE-3+	0 (0.000%)	0 (0.000%)	AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC
+
+total_reads: 2471

example/2.adapter.stat

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+adapter_id	polluted_reads	empty_reads	adapter_sequence
+iPE-5-	3 (0.121%)	0 (0.000%)	AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTA
+
+total_reads: 2471

example/iPE-3.fa

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+>iPE-3+
+AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC

example/iPE-5.fa

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+>iPE-5-
+AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTA

example/test1.sh

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+#!/bin/sh
+#$ -S /bin/sh
+#Version1.0	[email protected]	2018-02-08
+echo Start Time : 
+date
+../bin/fqcheck	-InFq1	B_1.fq.gz	-InFq2	B_2.fq.gz	-OutStat1	1	-OutStat2	2.fqcheck	
+echo End Time : 
+date

example/test2.sh

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+#!/bin/sh
+#$ -S /bin/sh
+#Version1.0	[email protected]	2018-02-08
+echo Start Time : 
+date
+../bin/fqcheck	-r	B_1.fq.gz	-c	1	
+echo End Time : 
+date

example/test3.sh

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+#!/bin/sh
+#$ -S /bin/sh
+#Version1.0	[email protected]	2018-02-08
+echo Start Time : 
+date
+../bin/fqcheck	-InFq1	B_1.fq.gz	-OutStat1	1.fqcheck	-InFq2	B_2.fq.gz	-OutStat2	2	-Adapter1	iPE-3.fa	-Adapter2	iPE-5.fa	
+echo End Time : 
+date

make.sh

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+#!/bin/sh
+#$ -S /bin/sh
+#Version1.0	[email protected]	2018-02-8
+echo Start Time : 
+date
+echo g++	-O3	-g	src/fqcheck.cpp  	-L ./lib	-lz	-o	bin/fqcheck -static	
+g++	-O3	-g	src/fqcheck.cpp	   -L	/zfssz5/BC_PUB/Software/01.Usr/lib/  -I ./include/ -L ./lib	-lz	-o	bin/fqcheck	 -static 
+echo End Time : 
+date