Formatting README

README.FastGT.md

@@ -11,27 +11,61 @@ FastGT has two binaries - gmer_counter and gmer_caller. Pre-compiled binaries ar
 
 * Compilation  
 Change int src subdirectory and type:
-'''
+```
 make gmer_counter
 make gmer_caller
-'''
+```
 
-* Usage
-
-First one has to prepare the database of specific k-mers for each allele of polymorphism of interest.
+* Usage   
+First one has to prepare the database of specific k-mers for each allele of polymorphism of interest.  
 k-mer databases are available from http://bioinfo.ut.ee/FastGT/  
 
 K-mers are counted from raw reads in FASTQ file using program gmer_counter:  
-'''
+```
 gmer_counter -db DATABASE FASTQ_FILE(S) > COUNTS_FILE.txt
-'''
+```
 
 Then the genotypes are called using program gmer_caller:  
-'''
+```
 gmer_caller COUNTS_FILE.txt > GENOTYPE_FILE.txt
-'''
+```
 
-Genotype file can be converted to VCF format:
-'''
+Genotype file can be converted to VCF format:  
+```
 generate_vcf.pl GENOTYPE_FILE.txt > GENOTYPE_FILE.vcf
-'''
+```
+
+Additional options for gmer_counter:   
+```
+    -db DATABASE     - SNP/KMER database file
+    -dbb DBBINARY    - binary database file
+    -w FILENAME      - write binary database to file
+    -32              - use 32-bit integeres for counts (default 16-bit)
+    --max_kmers NUM  - maximum number of kmers per node
+    --header         - print header row
+    --total          - print the total number of kmers per node
+    --unique         - print the number of nonzero kmers per node
+    --kmers          - print individual kmer counts (default if no other output)
+    --compile_index  - Add read index to database and write it to file
+    --distribution NUM  - print kmer distribution (up to given number)
+    --num_threads    - number of worker threads (default 24)
+    --low_memory     - optimize for low memory usage
+    -D               - increase debug level
+```
+
+Additional options for gmer_caller:   
+```
+    --training_size NUM - Use NUM markers for training (default 100000)
+    --runs NUMBER       - Perfom NUMBER runs of model training (use 0 for no training)
+    --num_threads NUM   - Use NUM threads (min 1, max 32, default 16)
+    --header            - Print table header
+    --non_canonical     - Output non-canonical genotypes
+    --prob_cutoff       - probability cutoff for calling genotype (default 0)
+    --alternatives      - Print probabilities of all alternative genotypes
+    --info              - Print information about individual
+    --no_genotypes      - Print only summary information, not actual genotypes
+    --model TYPE        - Model type (full, diploid, haploid)
+    --params PARAMS     - Model parameters (error, p0, p1, p2, coverage, size, size2)
+    --coverage NUM      - Average coverage of reads
+    -D                  - increase debug level
+```

README.GenomeTester4.md

@@ -1,75 +1,73 @@
-GenomeTester4 package
+# GenomeTester4 package
 
 GenomeTester4 is a toolkit for creating and manipulating k-mer lists. It
 contains 3 programs: glistmaker, glistcompare and glistquery. It is
 developed by Department of Bioinformatics, University of Tartu and
-distributed under GPL version 3.0 (or later).
-
-
-1. Quick usage for the impatient
-
-
-
+distributed under GPL version 3.0 (or later).  
+
+1. Quick usage for the impatient  
+```
   glistmaker|glistcompare|glistquery -h
+```
+Prints out quick description of command line arguments  
+
 
-Prints out quick description of command line arguments
-
-
-
+```
   glistmaker FASTA_FILES -w WORD_LENGTH -o OUTPUT_NAME
-
+```
 Generates a list of all unique k-mers in input files with their frequencies. The output file is
-named OUTPUT_NAME_WORD_LENGTH_0_0.list
-
-
-
+named OUTPUT_NAME_WORD_LENGTH_0_0.list  
+  
+  
+```
   glistquery LIST_FILE
-
-Prints out all k-mers and their frequencies in list file
-
-
-
+```
+Prints out all k-mers and their frequencies in list file  
+  
+  
+```
   glistquery LIST_FILE -q WORD
-
-Prints out the frequency of given word in list file
-
-
-
+```
+Prints out the frequency of given word in list file  
+  
+  
+```
   glistquery LIST_FILE -f WORD_FILE
-
-Prints out the frequencies of all words in WORD_FILE in list file
-
-
-
+```
+Prints out the frequencies of all words in WORD_FILE in list file  
+  
+  
+```
   glistcompare LIST_FILE_1 LIST_FILE_2 --union -o OUTPUT_NAME
-
+```
 Generates union of all words in both input lists. The frequencies in final
-list are sums of both input frequencies.
-
-
-
+list are sums of both input frequencies.  
+  
+  
+```
   glistcompare LIST_FILE_1 LIST_FILE_2 --intersection -o OUTPUT_NAME
-
-Generates intersection of words in both input lists. The frequencies in
-final list are smaller frequencies of either list
-
-
-
+```
+Generates intersection of words in both input lists. The frequencies in  
+final list are smaller frequencies of either list  
+  
+  
+```
   glistcompare LIST_FILE_1 LIST_FILE_2 --difference -o OUTPUT_FILE
-
+```
 Generates complement (words in the first file and NOT in second file) of
 words in both input lists. The frequencies in final list are the original
-frequencies in the first list.
-
-
-
-2. Compiling
-
+frequencies in the first list.  
+  
+  
+  
+2. Compiling  
+  
 GenomeTester4 is written in standard C. The only external dependency should
-be pthreads library that is standard in all Linux systems.
-Binaries compiled with full optimization are included in directory "bin".
+be pthreads library that is standard in all Linux systems.  
+Binaries compiled with full optimization are included in directory "bin".  
 If you for whatever reason have to compile these manually, just enter into
-src subdirectory and type:
-
+src subdirectory and type:  
+```
 make clean
 make
+```