update readme

README.md

@@ -11,7 +11,7 @@ libz >= 1.2.3
 ```
 To compile the SeqOthello tool chain, decompress the source code and execute the following commands in the source folder.
 ```
-./build.sh
+./compile.sh
 ```
 Then you can find the compile resutls in the ```build/bin``` folder. 
 
@@ -56,4 +56,4 @@ Use the following command to start a server on the machine, (e.g., on TCP port 3
 ```build/bin/Query --map-folder=out/ --start-server-port 3322```
 
 In another terminal, run the Client program.
-```build/bin/Client --transcript=kmer/test.fa --coverage --output=result --port=3333```
+```build/bin/Client --transcript=kmer/test.fa --coverage --output=result --port=3333```

genBuildFromJellyfishKmers.sh

@@ -33,7 +33,7 @@ TEMP_FOLDER="${INPUT:-`pwd`}"
 
 if [ ! -d ${TEMP_FOLDER}/bin ]; then 
     echo 'folder' ${TEMP_FOLDER}'/bin/ does not exist, creating.'
-    mkdir -p mkdir -p ${TEMP_FOLDER}/bin
+    mkdir -p ${TEMP_FOLDER}/bin
 fi
 
 
@@ -79,7 +79,7 @@ echo '        These group description files are' ${TEMP_FOLDER}/${BINARY_LIST_PR
 
 if [ ! -d ${TEMP_FOLDER}/grp ]; then 
     echo 'folder' ${TEMP_FOLDER}'/grp/ does not exist, creating.'
-    mkdir -p mkdir -p ${TEMP_FOLDER}/grp
+    mkdir  -p ${TEMP_FOLDER}/grp
 fi
 
 MAKE_GROUP=MakeGroup.sh
@@ -114,7 +114,7 @@ EXPORT_FOLDER="${INPUT:-$EXPORT_FOLDER_DEFAULT}"
 
 if [ ! -d ${EXPORT_FOLDER} ]; then 
     echo 'folder' ${EXPORT_FOLDER} 'does not exist, creating.'
-    mkdir -p mkdir -p ${EXPORT_FOLDER}
+    mkdir -p ${EXPORT_FOLDER}
 fi
 
 while [ ! -d ${KMER_PATH} ]; do 

genExample.sh

@@ -1,7 +1,7 @@
 #!/bin/bash
 mkdir -p kmer
 cd kmer
-../build/test/datagen -f 182 -k 15300 > genlog
+../build0/test/datagen -f 182 -k 15300 > genlog
 echo '>xxxxxxxxx|yyyyyyyyyy' > test.fa
 tail -n 1 genlog >> test.fa
 ls -m1 *.Kmer > flist