preparing for releast v1.2: update docs and up toml to 1.2

Project.toml

@@ -2,7 +2,7 @@ name = "MendelImpute"
 uuid = "e47305d1-6a61-5370-bc5d-77554d143183"
 keywords = ["Imputation"]
 authors = ["Benjamin Chu <[email protected]>", "Eric Sobel <[email protected]>", "Hua Zhou <[email protected]>"]
-version = "1.1.0"
+version = "1.2.0"
 
 [deps]
 BGEN = "6db4b851-9beb-4b83-9d64-eb1cfb37721d"
@@ -36,10 +36,8 @@ StatsPlots = "0.14"
 
 [extras]
 BenchmarkTools = "6e4b80f9-dd63-53aa-95a3-0cdb28fa8baf"
-CSV = "336ed68f-0bac-5ca0-87d4-7b16caf5d00b"
-DataFrames = "a93c6f00-e57d-5684-b7b6-d8193f3e46c0"
 Statistics = "10745b16-79ce-11e8-11f9-7d13ad32a3b2"
 Test = "8dfed614-e22c-5e08-85e1-65c5234f0b40"
 
 [targets]
-test = ["Test", "CSV", "BenchmarkTools", "Statistics", "DataFrames"]
+test = ["Test", "BenchmarkTools", "Statistics"]

docs/src/index.md

@@ -10,7 +10,7 @@ Given a target genotype file (phased or unphased and may contain missing data) a
 
 - Phasing and imputation with respect to a reference haplotype panel
 - Imputation on dosage data, phasing without imputation, imputation without phasing
-- Built-in support for [VCF](https://samtools.github.io/hts-specs/VCFv4.3.pdf) (`.vcf`, `.vcf.gz`), [PLINK](https://www.cog-genomics.org/plink2/formats#bed), and [BGEN](https://www.well.ox.ac.uk/~gav/bgen_format/)  (`.bgen`, currently experimental) files
+- Built-in support for [VCF](https://samtools.github.io/hts-specs/VCFv4.3.pdf) (`.vcf`, `.vcf.gz`), [binary PLINK](https://www.cog-genomics.org/plink2/formats#bed) (`.bed/.bim/.fam`), and [BGEN](https://www.well.ox.ac.uk/~gav/bgen_format/) (`.bgen`) files
 - Out-of-the-box multithreaded (shared memory) parallelism. 
 - Admixture estimation, with code examples to make pretty plots!
 - Ultra-compressed file for phased genotypes.

docs/src/man/Phasing_and_Imputation.ipynb

@@ -6,10 +6,11 @@
    "source": [
     "# Preparing Target Data\n",
     "\n",
-    "MendelImpute accepts [VCF](https://samtools.github.io/hts-specs/VCFv4.3.pdf) and [PLINK (.bed/.bim/.fam)](https://www.cog-genomics.org/plink2/formats#bed), and [BGEN](https://www.well.ox.ac.uk/~gav/bgen_format/) files. Please make sure the following are true:\n",
+    "MendelImpute accepts [VCF](https://samtools.github.io/hts-specs/VCFv4.3.pdf), [PLINK (.bed/.bim/.fam)](https://www.cog-genomics.org/plink2/formats#bed), and [BGEN](https://www.well.ox.ac.uk/~gav/bgen_format/) files.  Please make sure the following are true:\n",
     "\n",
-    "+ VCF file ends in `.vcf` or `.vcf.gz` (phased or unphased and may contain missing data)\n",
-    "+ BGEN file ends in `.bgen` (if used to store haplotypes, all variants must be phased and non-missing). \n",
+    "+ Missing data is allowed. Genotypes does not have to be phased. \n",
+    "+ VCF file ends in `.vcf` or `.vcf.gz`\n",
+    "+ BGEN file ends in `.bgen`. If available, index files should have the same prefix. (e.g. `genotypes.bgen` should have index file called `genotypes.bgen.bgi`. Sample identifiers may be either contained in the `.bgen` file or listed in an external `genotypes.sample` file.\n",
     "+ For PLINK files, all trios (`.bim`, `.bed`, `.fam`) are present in the same directory\n",
     "+ Each file contains only 1 (non-sex) chromosome\n",
     "+ Every record (SNP) in the imputation target is present in the reference panel. If this is untrue, you must [match markers in 2 VCF files](https://openmendel.github.io/VCFTools.jl/dev/man/conformgt/). \n",
@@ -22,7 +23,6 @@
    "metadata": {},
    "source": [
     "    !!! note\n",
-    "\n",
     "Currently only BGEN inputs support index files. Indexing support for VCF files coming soon..."
    ]
   },

docs/src/man/Phasing_and_Imputation.md

@@ -1,18 +1,18 @@
 
 # Preparing Target Data
 
-MendelImpute accepts [VCF](https://samtools.github.io/hts-specs/VCFv4.3.pdf) and [PLINK (.bed/.bim/.fam)](https://www.cog-genomics.org/plink2/formats#bed), and [BGEN](https://www.well.ox.ac.uk/~gav/bgen_format/) files. Please make sure the following are true:
+MendelImpute accepts [VCF](https://samtools.github.io/hts-specs/VCFv4.3.pdf), [PLINK (.bed/.bim/.fam)](https://www.cog-genomics.org/plink2/formats#bed), and [BGEN](https://www.well.ox.ac.uk/~gav/bgen_format/) files.  Please make sure the following are true:
 
-+ VCF file ends in `.vcf` or `.vcf.gz` (phased or unphased and may contain missing data)
-+ BGEN file ends in `.bgen` (if used to store haplotypes, all variants must be phased and non-missing). 
++ Missing data is allowed. Genotypes does not have to be phased. 
++ VCF file ends in `.vcf` or `.vcf.gz`
++ BGEN file ends in `.bgen`. If available, index files should have the same prefix. (e.g. `genotypes.bgen` should have index file called `genotypes.bgen.bgi`. Sample identifiers may be either contained in the `.bgen` file or listed in an external `genotypes.sample` file.
 + For PLINK files, all trios (`.bim`, `.bed`, `.fam`) are present in the same directory
 + Each file contains only 1 (non-sex) chromosome
 + Every record (SNP) in the imputation target is present in the reference panel. If this is untrue, you must [match markers in 2 VCF files](https://openmendel.github.io/VCFTools.jl/dev/man/conformgt/). 
 + Given a SNP, its CHROM, POS, REF, and  ALT fields are the same in target data and reference panel. MendelImpute use SNP position internally to align markers. 
 + The position of every SNP is unique: so multiallelic markers should be excluded instead of split (this requirement will eventually be lifted). 
 
     !!! note
-
 Currently only BGEN inputs support index files. Indexing support for VCF files coming soon...
 
 # Preparing Reference Haplotype Panel