update document on qbasepileup

[ChristinaXu2017]

Description

qbasepileup seems dated, the usage description is not related to some misleading descriptions. After several tests, usage and option descriptions are updated. Fixes #303 #304 #305
The document is updated also, compound SNP mode and indel mode are highlighted as deprecated due to the input formate is no longer exists.

The new help message is here:

Option                   Description                                                                             
------                   -----------                                                                             
-V, -v, --version        Print version info.                                                                     
-b <txt file>            Opt (coverage and snp mode),  path to tab delimited file with list of bams.             
--bq <Integer>           Opt (snp related mode), minimum base quality score for accepting a read. Def = null.    
--dup                    Opt (indel and snp mode), a flag to include duplicates reads.                           
-f [format]              Opt(snp mode) snp file format: [dcc1, dccq, vcf, tab, maf].Def=dcc1. or                 
                         Opt(coverage mode), snp file format: [dcc1, dccq, vcf, tab, maf, gff3, gtf]. Def=dcc1.  
--filter <query>         Opt, a qbamfilter query to filter out BAM records. Def=null.                            
--gatk                   Opt (indel mode), a flag to conform gatk format, but do nothing.                        
-h, --help               Shows this help message.                                                                
--hdf <hdf file>         Opt (snp mode), path to hdf file which header contains a list of bams.                  
--hp <Integer>           Opt (indel mode), base around indel to check for homopolymers. Def=10.                  
-i <bam file>            Opt (coverage and snp mode), specify a single SAM/BAM file here.                        
--ig <dcc1>              Req (indel mode), path to germline indel file in dcc1 format.                           
--in <bam file>          Req (indel mode), path to normal bam file                                               
--ind <y|n>              Opt (snp related mode), include reads with indels [y,n]. Def=y.                         
--intron <y|n>           Opt (snp related mode), include reads mapping across introns [y,n]. Def=y.              
--is <dcc1>              Req (indel mode), path to somatic indel file in dcc1 format.                            
--it <bam file>          Req (indel mode), path to tumour bam file                                               
--log                    Req, log file.                                                                          
--loglevel               Opt, logging level required, e.g. INFO, DEBUG. Default INFO.                            
-m <mode>                Opt, Mode [snp, compoundsnp, snpcheck, indel, coverage]. Def=snp.                       
--mincov <Integer>       Opt, report reads that are less than the mininmum coverage option.                      
--mq <Integer>           Opt (snp related mode), minimum mapping quality score for accepting a read. Def = null. 
-n <Integer>             Opt (indel mode), bases around indel to check for other indels. Def=3.                  
--novelstarts <y|n>      Opt (snp related mode), report novelstarts rather than read count [Y,N], Def=y.         
-o <txt file>            Req (coverage and snp related mode), the output file path.                              
--of <format>            Opt (snp mode only), output file format [columns]. this option only works with input snp
                           file format is tab, otherwise it will ignored.                                        
--og <dcc1>              Req (indel mode), output file for germline indels.                                      
--os <dcc1>              Req (indel mode), output file for somatic indels.                                       
-p [profile]             Opt (snp mode), pileup profile type [torrent,RNA,DNA, standard]. Def="standard".        
--pd <pindel_deletions>  Req (indel mode), path to normal bam file                                               
--pindel                 Opt (indel mode), a flag to conform pindel format, but do nothing.                      
-r <fasta file>          Req (indel and snp mode), path to reference genome fasta file.                          
-s <txt file>            Req (coverage and snp mode), path to tab delimited file containing snps.                
--sc <Integer>           Opt (indel mode), bases around indel to check for softclip. Def=13.                     
--strand <y|n>           Opt (snp related mode), separate coverage by strand [y,n]. Def=y.                       
--strelka                Opt (indel mode), a flag to conform strelka format, but do nothing.                     
-t [Integer]             Opt, number of worker threads (yields n+2 total threads). Def=1.         

Type of change

document and option description only!

How Has This Been Tested?

nil

Are WDL Updates Required?

nil

Checklist:

nil

[holmeso]

dated or deprecated?

[ChristinaXu2017]

I am waiting for JP's decision. the indel and compound SNP modes are deprecated but the SNP and coverage mode still work OK.