update README

README.md

@@ -55,13 +55,13 @@ python setup.py install
 ```
 If you would like to install methylpy in path of your choice, run 
 `python setup.py install --prefix=/USER/PATH/`. 
-Then, try `methylpy` and if it gives no error, the setup is likely successful.
+Then, try `methylpy` and if no error pops out, the setup is likely successful.
 See [Test methylpy](#test-methylpy) for more rigorious test.
-Last, processing large dataset will require space for storing temporary files. However,
-the default directory is unlikely to fit the need.
-You may want to set the `TMPDIR` environmental variable to the absolute path of a directory
-on hard drive with sufficient space (e.g. `/YOUR/TMP/DIR/`). This can be done by adding the 
-below command to ~/.bashrc file: `export TMPDIR=/YOUR/TMP/DIR/`.
+Last, processing large dataset will require large spare space for temporary files.
+Usually, the default directory for temporary files will not meet the need.
+You may want to set the `TMPDIR` environmental variable to the (absolute) path of a directory
+on hard drive with sufficient space (e.g. `/YOUR/TMP/DIR/`). This can be done by adding the
+below command to `~/.bashrc file`: `export TMPDIR=/YOUR/TMP/DIR/` and run `source ~/.bashrc`.
 
 #### Step 2 - Install dependencies
 python is required for running methylpy. Both python2 (>=2.7.9) and python3 (>=3.6.2) will work.
@@ -104,9 +104,18 @@ g++ -o run_rms_tests.out rms.cpp `gsl-config --cflags —libs`
 # Test methylpy
 To test whether methylpy and the dependencies are installed and set up correctly, run
 ```
-cd methylpy/test
+wget http://neomorph.salk.edu/yupeng/share/methylpy_test.tar.gz
+tar -xf methylpy_test.tar.gz
+cd methylpy_test/
 python run_test.py
 ```
+The test should take around 3 minutes, and progress will be printed on screen. After the test is started,
+two files `test_output_msg.txt` and `test_error_msg.txt` will be generated. The former
+contains more details about each test and the later stores error message (if any) as well as additional
+information.
+
+If test fails, please check `test_error_msg.txt` for the error message. If you decide to submit an issue
+regarding test failure to methylpy github page, please include the error message in this file.
 
 # Process data
 Please see [methylpy tutorial](https://github.com/yupenghe/methylpy/blob/methylpy/tutorial.md)

methylpy/call_mc_pe.py

@@ -757,7 +757,7 @@ def find_multi_mappers_pe(inputf,output,num_procs=1,
  mapped reads) and True for the second. This option is mainly for safety. It ensures that files from
  previous runs are erased.
  """
- min_mapq = max(2,min_mapq)
+ min_mapq = max(3,min_mapq)
  sam_header = []
  file_handles = {}
  f = open(inputf,'r')