README.md in bio-polyploid-tools-0.6.0 vs README.md in bio-polyploid-tools-0.6.1

@@ -1,45 +1,59 @@
-bio-polyploid-tools
-===================
+#bio-polyploid-tools
 
-Introduction
--------------
+##Introduction
 This tools are designed to deal with polyploid wheat. The first tool is to design KASP primers, 
 making them as specific as possible. 
 
 
-Installation
-------------
-'gem install bio-polyploid-tools'
+##Installation
+```sh
+gem install bio-polyploid-tools
+```
+You need to have in your ```$PATH``` the following programs:
 
-You need to have in your $PATH the following programs:
-* [MAFFT]{http://mafft.cbrc.jp/alignment/software/}
-* [primer3]{http://primer3.sourceforge.net/releases.php}
-* [exonerate]{http://www.ebi.ac.uk/~guy/exonerate/} 
+* [MAFFT](http://mafft.cbrc.jp/alignment/software/)
+* [primer3](http://primer3.sourceforge.net/releases.php)
+* [exonerate](http://www.ebi.ac.uk/~guy/exonerate/) 
 
 The code has been developed on ruby 2.1.0, but it should work on 1.9.3 and above. 
 
 
-Polymarker
-----------
+#PolyMarker
 
 To run poolymerker with the CSS wheat contigs, you need to unzip the 
-reference file [Triticum_aestivum.IWGSP1.22.dna_rm.genome.fa.gz{ftp://ftp.ensemblgenomes.org/pub/release-22/plants/fasta/triticum_aestivum/dna/}. 
+(reference file)[ftp://ftp.ensemblgenomes.org/pub/release-25/plants/fasta/triticum_aestivum/dna/Triticum_aestivum.IWGSC2.25.dna.genome.fa.gz
+].
 
-polymarker.rb --contigs Triticum_aestivum.IWGSP1.22.dna_rm.genome.fa --marker_list snp_list.csv --output output_folder
 
+
+```sh
+polymarker.rb --contigs Triticum_aestivum.IWGSC2.25.dna.genome.fa --marker_list snp_list.csv --output output_folder
+```
+
 The snp_list file must follow the convention
 <ID>,<Chromosome>,<SEQUENCE>
 with the SNP inside the sequence in the format [A/T]. As a reference, look at test/data/short_primer_design_test.csv
 
-Notes
------
+If you want to use the web interface, visit the [PolyMarker webservice at TGAC](http://polymarker.tgac.ac.uk)
 
+##Release Notes
+
+###0.6.1
+
+
+* polymarker.rb now validates that all the files exist. 
+* BUGFIX: A reference was required even when it was not used to generate contigs. 
+
+#Notes
+
+
 * If the SNP is in a gap in the alignment to the chromosomes, it is ignored. 
 
 BUG: Blocks with NNNs are picked and treated as semi-specific. 
 BUG: If the name of the reference have space, the ID is not chopped. ">gene_1 (G12A)" shouls be treated as ">gene_1". 
-TODO: If reading from a reference file, only get one reference to align when the region is queried several times
 TODO: Add a parameter file to configure the alignments. 
 TODO: Produce primers for products of different sizes
+
+