Huayan

Hi Peter, 

I fixed some errors with "full parameter settings". And also the SMD submodules can run as a workflow. For details, please see the following txt file:

Mar. 4, 2013
Pending bugs:
1. soap1:
The parameter -t (read_id) for full parameter settings will lead to an endless loop, so removed this paramter for now. 

2. soapsnp
The parameter -q for full parameter settings will lead to an empty output so
an error too. Removed for now. 

3. soapdenovo2
The parameter -m (max_k if multi-kmer) is removed due to error.

4. soapdenovo-trans
"reads only used for scaffold assembly" not working
May need to rewrite this tool. 


Solved issues:
1. Scaff Submodule
Parameter -z was removed from the command since no such one exists. 

2. SoapCoverage:
working now. 

3. SOAPSNV package 
Able to run the output from one to another, as a workflow.