Improve readme and add a license

LICENSE

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+The MIT License (MIT)
+
+Copyright (c) 2015 Karel Břinda
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.
+

README.md

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+# OCOCO - Online Consensus Caller
+
+## Prerequisities
+
+* C++ compiler
+* CMake
+
+## Getting started
+
+```bash
+git clone https://github.com/karel-brinda/ococo
+cd ococo && cmake . && make
+./ococo -i test.bam -f test.fa -m real-time --vcf-cons -
+```
+
+## Command line parameters
+
+```
+Generic options:
+  -v [ --version ]                      Print version and exit.
+  -h [ --help ]                         Print this message and exit.
+
+Input options:
+  -i [ --input ] arg                    Input SAM/BAM file (- for standard
+                                        input).
+  -f [ --fasta-ref ] arg                Initial FASTA reference (if not
+                                        provided, sequence of N's is considered
+                                        as the reference).
+  -s [ --stats-in ] arg                 Input statistics.
+
+Output options:
+  -F [ --fasta-cons ] arg               FASTA file with consensus.
+  -S [ --stats-out ] arg                Outputs statistics.
+  -V [ --vcf-cons ] arg                 VCF file with updates of consensus (-
+                                        for standard output).
+  -P [ --pileup ] arg                   Truncated pileup (- for standard
+                                        output).
+  --verbose                             Verbose mode.
+
+Parameters of consensus calling:
+  -x [ --counters ] arg (=ococo16)      Counters configuration:
+                                         - ococo16 (3 bits per counter)
+                                         - ococo32 (7 bits per counter)
+                                         - ococo64 (15 bits per counter)
+  -m [ --mode ] arg (=batch)            Mode: real-time / batch.
+  -t [ --strategy ] arg (=majority)     Strategy for updates: no-updates /
+                                        majority / stochastic.
+  -a [ --allow-amb ]                    Allow updates to ambiguous nucleotides.
+  -q [ --min-MQ ] arg (=1)              Skip alignments with mapping quality
+                                        smaller than INT.
+  -Q [ --min-BQ ] arg (=13)             Skip bases with base quality smaller
+                                        than INT.
+  -w [ --ref-weight ] arg (=0)          Initial counter value for nucleotides
+                                        from the reference.
+  -c [ --min-coverage ] arg (=2)        Minimum coverage required for update.
+  -M [ --majority-threshold ] arg (=0.59999999999999998)
+                                        Majority threshold.
+```