Add README and LICENCE + requirements file

README.md

+Miniannotator
+=============
+
+A tool for identifying genes and introns based on mapping of De novo RNA-seq contigs on a reference genome.
+
+This tools also identify indels between the contigs and the reference genome.
+
+
+How it works?
+--------------
+
+1. [Minimap2](https://github.com/lh3/minimap2) is used to map contigs on the reference genome.
+
+2. We parse matches and get all of them with at least 90% of their sequence matching the reference (this value can be customized)
+
+3. For each contig:
+    - mapping bounds defines the gene position
+    - splits defines the exons: the N are the intron, matching part are the exons
+    - we save all indels from CIGAR string
+    
+4. Save all genes, exons and indels into an unique GTF file
+
+
+Requirements
+------------
+
+This program requires at least Python 3.5.
+
+Some python modules are required:
+
+- pysam == 0.14.*
+- PyYAML == 3.13
+
+Install them in one command line:
+
+    pip3 install -r requirements.txt
+
+
+How to use?
+-----------
+
+    ./miniannotator.py -r {reference_file} -a {contigs} -o {output_folder}
+
+with:
+
+`reference_file`: path to the reference fasta file  
+`contigs`: path to the contigs fasta file  
+`output_folder`: path to the output folder where results will be stored. If not exists, will be created.
+
+### Optional arguments
+
+`-m {map}`: give your bam file to the program, if already computed. It will be used instead of building it with minimap
+
+`-q {min-overlap}`: set the minimum percent size of the contig which needs to match the reference (other matches will be ignored). Default: 90.
+
+
+Configuration
+-------------
+
+If minimap2 or samtools is not in your PATH, set in miniannotator.yml their path.
+
+You can also define the number of threads to use for minimap2.
\ No newline at end of file

requirements.txt

+pysam==0.14.1
+PyYAML==3.13