bug fix

.gitignore

@@ -0,0 +1,4 @@
+maven-src/.idea
+maven-src/target
+maven-src/out
+

README.md

@@ -1,5 +1,5 @@
 # HAlign-II
-HAlign-II is a software based Java, which can align multiple DNA/RNA/Protein sequences in stand-alone mode or Hadoop cluster mode. Hadoop parallel computing environment has a faster alignment speed. Additionally, if a Hadoop cluster environment is not ready, you can use its stand-alone mode to start your work. But when your sequence files are large (more than 1GB), we recommend that you'd better to run on the Hadoop cluster to save valuable time.
+HAlign-II is a Java based software, which can align multiple nuleotide/protein sequences stand-alone on Hadoop cluster. Hadoop parallel computing environment has a faster alignment speed. Additionally, if a Hadoop cluster environment is not ready, you can use its stand-alone mode to start your work. But when your sequence files are large (more than 1GB), we recommend that you'd better to run on the Hadoop cluster to save valuable time.
 
 Home page: http://lab.malab.cn/soft/halign   
 Reference: Shixiang Wan and Quan Zou, HAlign-II: efficient ultra-large multiple sequence alignment and phylogenetic tree reconstruction with distributed and parallel computing, Algorithms for Molecular Biology, 2017, 12:25. [view](https://almob.biomedcentral.com/articles/10.1186/s13015-017-0116-x)
@@ -42,12 +42,12 @@ Other implementations:
   * algorithm: sequence alignment algorithms, required for **-sparkMSA** mode, but none for **-sparkTree** mode. **0** represents the suffix tree algorithm, the fastest, but only for DNA/RNA; **1** represents the KBand algorithm based BLOSUM62 scoring matrix, only for Protein.
 
 # Update
-* 2016-09-07, version 2.0.0:
-  * Basic functions.
-* 2016-11-14, version 2.1.0:
-  * Add version: comment for english.
+* 2020-07-16, version 2.1.2:
+  * bug fix
 * 2016-11-25, version 2.1.1:
   * Fix some bugs about protein sequences alignment on multi-thread technique.
   * Fix some bugs about file I/O.
-* 2017-10-12, version 2.1.1:
-  * update README.
+* 2016-11-14, version 2.1.0:
+  * Add version: comment for english.
+* 2016-09-07, version 2.0.0:
+  * Basic functions.