documentation improvement

Author: Beifang

README.md

@@ -1,6 +1,6 @@
 MSIsensor
 ===========
-Homopolymer and microsatellite analysis using bam files
+MSIsensor, a c++ program for automatically detecting somatic microsatellite changes. It computes length distributions of microsatellites per site in paired tumor and normal sequence data, subsequently using these to statistically compare observed distributions in both samples. Comprehensive testing indicates MSIsensor is an efficient and effective tool for deriving MSI status from standard tumor-normal paired sequence data.
 
 Usage
 -----
@@ -13,8 +13,41 @@ Key commands:
         scan            scan homopolymers and miscrosatelites
         msi             msi scoring
 
-This tool was originally designed to do homopolymer and microsatellites analysis. 
-
+msisensor scan [options]:
+       
+       -d   <string>   reference genome sequences file, *.fasta format
+       -o   <string>   output homopolymer and microsatelittes file
+
+       -l   <int>      minimal homopolymer size, default=5
+       -c   <int>      context length, default=5
+       -m   <int>      maximal homopolymer size, default=50
+       -s   <int>      maximal length of microsate, default=5
+       -r   <int>      minimal repeat times of microsate, default=3
+       -p   <int>      output homopolymer only, 0: no; 1: yes, default=0
+       
+       -h   help
+ 
+msisensor msi [options]:
+
+       -d   <string>   homopolymer and microsates file
+       -n   <string>   normal bam file
+       -t   <string>   tumor  bam file
+       -o   <string>   output distribution file
+
+       -e   <string>   bed file
+       -r   <string>   choose one region, format: 1:10000000-20000000
+       -l   <int>      mininal homopolymer size, default=5
+       -p   <int>      mininal homopolymer size for distribution analysis, default=10
+       -m   <int>      maximal homopolymer size for distribution analysis, default=50
+       -q   <int>      mininal microsates size, default=3
+       -s   <int>      mininal microsates size for distribution analysis, default=5
+       -w   <int>      maximal microstaes size for distribution analysis, default=40
+       -u   <int>      span size around window for extracting reads, default=500
+       -b   <int>      threads number for parallel computing, default=1
+       -x   <int>      output homopolymer only, 0: no; 1: yes, default=0
+       -y   <int>      output microsatellite only, 0: no; 1: yes, default=0
+       
+       -h   help
 
 Install
 -------
@@ -42,5 +75,62 @@ I recommend dumping it in the system directory for locally compiled packages:
 
     sudo mv msisensor /usr/local/bin/
 
-xxx
+Example
+-------
+1. Scan microsatellites from reference genome:
+  
+        msisensor scan -d referen.fa -o microsatellites.list
+
+2. Msi scorring: 
+
+        msisensor msi -d microsatellites.list -n normal.bam -t tumor.bam -e bed.file -o output.prefix -l 1 -q 1 -b 2
+
+
+Output
+-------
+There will be one microsatellite list output in "scan" step. 
+Msi scorring step will give 4 output files based on given output prefix:
+    output.prefix
+    output.prefix_dis
+    output.prefix_germline
+    output.prefix_somatic
+
+1. microsatellites.list: microsatellite list output 
+
+    chromosome      location        site_length     site_content    repeat_times    front_flank     tail_flank      site_bases      front_flank_bases       tail_flank_bases
+    1       10485   4       149     3       150     685     GCCC    AGCCG   GGGTC
+    1       10629   2       9       3       258     409     GC      CAAAG   CGCGC
+    1       10652   2       2       3       665     614     AG      GGCGC   GCGCG
+    1       10658   2       9       3       546     409     GC      GAGAG   CGCGC
+    1       10681   2       2       3       665     614     AG      GGCGC   GCGCG
+
+2. output.prefix: msi score output
+
+    Total_Number_of_Sites   Number_of_Somatic_Sites %
+    640     75      11.72
+
+3. output.prefix_dis: read count distribution (N: normal; T: tumor)
+
+    1 10529896 CTTTC 15[T] GAGAC
+    N: 0 0 0 0 0 0 0 1 0 0 8 9 1 7 17 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 
+    T: 0 0 0 0 0 0 0 0 0 1 19 14 17 9 32 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 
+
+4. output.prefix_somatic: somatic sites detected
+  
+    chromosome   location        front_flank     repeat_times    site_content    tail_flank      difference      P_value
+    1       10357206        TTGAA   17      T       ACTTC   0.45670 0.00014
+    1       11140610        TCTGG   11      A       CACAC   0.80855 0.00000
+    1       11156045        ACATC   15      T       GAGAC   0.75281 0.00001
+    1       12368705        GAGTG   15      T       GAGAT   0.51139 0.00000
+    1       16200729        TAAGA   10      T       CTTGT   0.55652 0.00000
+    1       16245610        AAGGG   10      T       GCATA   0.75928 0.00000
+
+5. output.prefix_germline: germline sites detected
+    
+    chromosome   location        front_flank     repeat_times    site_content    tail_flank      xxx|xxxx
+    1       1192105 AATAC   11      A       TTAGC   5|5
+    1       1330899 CTGCC   5       AG      CACAG   5|5
+    1       1598690 AATAC   12      A       TTAGC   5|5
+    1       1605407 AAAAG   14      A       GAAAA   1|1
+    1       2118724 TTTTC   11      T       CTTTT   1|1
 

distribution.cpp

@@ -65,7 +65,7 @@ std::ofstream foutD;
 std::string one_region;
 
 void DisUsage(void) {
-    std::cerr<<"\nUsage:  plolyscape dis [options] \n\n"
+    std::cerr<<"\nUsage:  msisensor msi [options] \n\n"
         <<"       -d   <string>   homopolymer and microsates file\n"
         <<"       -n   <string>   normal bam file\n"
         <<"       -t   <string>   tumor  bam file\n"

scan.cpp

@@ -52,7 +52,7 @@ std::ifstream fin_d;
 std::ofstream fout;
 
 void ScanUsage(void) {
-    std::cerr<<"\nUsage:  plolyscape scan [options] \n\n"
+    std::cerr<<"\nUsage:  msisensor scan [options] \n\n"
         <<"       -d   <string>   reference genome sequences file, *.fasta format\n"
         <<"       -o   <string>   output homopolymer and microsatelittes file\n\n"
         <<"       -l   <int>      minimal homopolymer size, default="<<param.MininalHomoSize<<"\n"