Add README for haploid case

README.md

@@ -1,2 +1,31 @@
 # lshmm
-code to run Li and Stephens
+**lshmm** is a Python library for prototyping, experimenting, and testing implementations of algorithms using the Li & Stephens (2003) Hidden Markov Model.
+
+## Usage
+
+### Inputs
+#### Data
+* Sample and/or ancestral haplotypes comprising a reference panel.
+* Query haplotypes.
+
+In the haploid mode, the alleles in haplotypes can be represented by any integer value (besides `-1` and `-2`, which are special values). In the diploid mode, the genotypes (encoded as allele dosages) can be `0` (homozygous for the reference allele), `1` (heterozygous for the alternative allele), or `2` (homozygous for the alternative allele). Currently, multiallelic sites are supported only in the haploid mode, but not the diploid mode.
+
+Note that there are two special values `NONCOPY` and `MISSING`. `NONCOPY` (or `-2`) represent non-copiable states, and can only be found in partial ancestral haplotypes in the reference panel. `MISSING` (or `-1`) representing missing data, and can be found only in query haplotypes.
+
+#### Parameters
+* Recombination probabilities.
+* Mutation probabilities.
+
+### Models and algorithms
+* Haploid LS HMM
+  * Forward-backward algorithm
+  * Viterbi algorithm
+* Diploid LS HMM
+  * Forward-backward algorithm
+  * Viterbi algorithm
+
+### Features
+* Scaling of mutation rate by the number of distinct alleles per site.
+* Non-copiable state in the reference panel (`NONCOPY`).
+* Missing state in the query (`MISSING`).
+* Multiallelic sites (haploid only).