Add build_vignettes install option to README

Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>

Author: jimb3

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: BinaryDosage
 Title: Creates, Merges, and Reads Binary Dosage Files
-Version: 1.0.0.9020
+Version: 1.0.0.9021
 Authors@R:
     c(person(given = "John",
              family = "Morrison",

README.Rmd

@@ -104,7 +104,7 @@ There are 4 formats for a binary dosage data set. Data sets in formats 1, 2, and
 # Installation
 
 1. Install the [devtools](https://github.com/r-lib/devtools) package
-2. Install the [BinaryDosage](https://github.com/USCbiostats/BinaryDosage) package directly from the USCbiostats repository on GitHub: 
+2. Install the [BinaryDosage](https://github.com/USCbiostats/BinaryDosage) package directly from the USCbiostats repository on GitHub:
 
 ``` {r, eval = F}
 remove.packages("BinaryDosage")
@@ -113,6 +113,14 @@ devtools::install_github("https://github.com/USCbiostats/BinaryDosage")
 library(BinaryDosage)
 ```
 
+To install the package with vignettes built, use the `build_vignettes` option:
+
+``` {r, eval = F}
+devtools::install_github("https://github.com/USCbiostats/BinaryDosage", build_vignettes = TRUE)
+
+library(BinaryDosage)
+```
+
 # Usage
 
 #### General Workflow

README.md

@@ -5,12 +5,73 @@ BinaryDosage: Creates, Merges, and Reads Binary Dosage Files
 
 [![AppVeyor build
 status](https://ci.appveyor.com/api/projects/status/github/USCbiostats/BinaryDosage?branch=master&svg=true)](https://ci.appveyor.com/project/USCbiostats/BinaryDosage)
+[![Travis build
+status](https://travis-ci.org/USCbiostats/BinaryDosage.svg?branch=master)](https://app.travis-ci.com/USCbiostats/BinaryDosage)
 [![Codecov test
 coverage](https://codecov.io/gh/USCbiostats/BinaryDosage/branch/master/graph/badge.svg)](https://app.codecov.io/gh/USCbiostats/BinaryDosage?branch=master)
 <!-- badges: end -->
 
 # Binary Dosage Files
 
+### Important News
+
+A new version of BinaryDosage has been developed that significantly
+reduces data read times by a factor of more than 10 times. This new
+version uses the hstlib libraries which greatly improves the read speed
+of VCF files. To compile this new version requires the installation of
+the
+[Rhtslib](https://bioconductor.org/packages/release/bioc/html/Rhtslib.html)
+library from Bioconductor.
+
+Data compression of the BinaryDosage formatted files has also been
+improved. We have had reports that the BinaryDosage formatted files were
+over 3 times larger than the gzipped VCF file. This was due to the
+compression routine not compressing SNPs with low minor allele
+frequencies (\<0.01) well. When BinaryDosage was first written,
+imputation servers did not include many rare SNPs. This has changed
+since BinaryDosage was first written.
+
+To install the latest version of BinaryDosage, it is recommended the
+user have R 4.3.x or higher. If the user is using Windows, they will
+need to verify that the current version of [R
+tools](https://cran.r-project.org/bin/windows/Rtools/) is installed. If
+the user is using Linux or Mac OS X, the zlib development tools need to
+be installed, often named zlib1g-dev. For most systems, these tools are
+usually already loaded.
+
+The package
+[Rhtslib](https://bioconductor.org/packages/release/bioc/html/Rhtslib.html)
+from BioConductor needs to be installed using the following code.
+
+``` r
+if (!require("BiocManager", quietly = TRUE))
+    install.packages("BiocManager")
+
+BiocManager::install("Rhtslib")
+```
+
+Once the preceding prerequisites are met the follow code will install
+the latest version of BinaryDosage.
+
+``` r
+remove.packages("BinaryDosage")
+devtools::install_github("https://github.com/USCbiostats/BinaryDosage@htslib")
+
+library(BinaryDosage)
+```
+
+#### Important
+
+All BinaryDosage formatted files created with older versions are fully
+compatible with this new version of BinaryDosage.
+[GxEScanR](https://github.com/USCbiostats/GxEScanR) works with files
+created by all versions of BinaryDosage, including this new one.
+
+The information below is for the current release version of
+BinaryDosage. Visit the [htslib
+branch](https://github.com/USCbiostats/BinaryDosage/tree/htslib) or
+BinaryDosage for more information about the new version.
+
 ### Introduction
 
 Genotype imputation is an essential tool in genomics, enabling
@@ -48,24 +109,23 @@ For GWAS/GWIS analysis of BinaryDosage files, please refer to the
   - Family ID
   - Subject ID
 - SNP information
-  - Chromosome number  
-  - SNP ID  
-  - Location in base pairs  
-  - Reference allele  
-  - Alternate allele  
+  - Chromosome number\
+  - SNP ID\
+  - Location in base pairs\
+  - Reference allele\
+  - Alternate allele\
 - Genetic information
   - Dosage values
   - Genotype probabilities, Pr(*g=0*), Pr(*g=1*), Pr(*g=2*)
 
-There are 5 formats for a binary dosage data set. Data sets in formats
+There are 4 formats for a binary dosage data set. Data sets in formats
 1, 2, and 3 have 3 files, a sample information file, a SNP information
 file, and a genetic information file. Data sets in format 4 have just 1
-file. Format 5 uses per-SNP gzip compression and stores metadata in a
-companion RDS file (`.bdose.bdi`), named by appending `.bdi` to the
-`.bdose` filename. This file contains all the information listed above
-and may contain the following information.
+file. This file contains all the information listed above and may
+contain the following information.
 
-**Note:** Format 5 is the recommended format for new data sets.
+**Note:** Format 4 is recommended and is the default value for all
+functions.
 
 - Additional SNP information
   - Alternate allele frequency
@@ -78,27 +138,27 @@ and may contain the following information.
 
 ### Functions
 
-#### Format 5 (recommended)
-
-- **vcftobd** - Converts a bgzipped VCF file to a Format 5 binary dosage data set (requires vcfppR)
-- **getbd5info** - Loads a Format 5 file pair and returns an R list (required for **getsnp**, **bdapply**, and **mergebd**)
-- **getbd5snp** - Reads a single SNP from a Format 5 file by index or ID
-- **updatebd** - Converts a legacy format (1–4) binary dosage file to Format 5
-- **subsetbd** - Creates a new Format 5 file containing a subset of SNPs and/or subjects from any binary dosage file (formats 1–5)
-- **mergebd** - Merges two or more Format 5 files into a single Format 5 file
-
-#### Legacy formats (1–4)
-
-- **vcftobdlegacy** - Converts a VCF file to a legacy format (1–4) binary dosage data set (deprecated; use **vcftobd** instead)
-- **gentobd** - Converts a GEN (impute2) file to a binary dosage data set
-- **bdmerge** - Merges multiple legacy binary dosage data sets into a single data set
-- **getbdinfo** - Creates an R list containing information about a binary dosage data set (required for **getsnp** and **bdapply**)
-- **getvcfinfo** - Creates an R list containing information about a VCF file (required for **vcfapply**)
-- **getgeninfo** - Creates an R list containing information about a GEN file (required for **genapply**)
-- **bdapply** - Applies a function to the data for each SNP in a binary dosage file (requires list returned by **getbdinfo** or **getbd5info**)
-- **vcfapply** - Applies a function to the data for each SNP in a VCF file (requires list returned by **getvcfinfo**)
-- **genapply** - Applies a function to the data for each SNP in a GEN file (requires list returned by **getgeninfo**)
-- **getsnp** - Returns dosage and genotype probabilities for a single SNP from a binary dosage file
+- **vcftobd** - Converts a VCF file to a Format 5 binary dosage data set
+- **vcftobdlegacy** - Converts a VCF file to a legacy format (1-4)
+  binary dosage data set
+- **gentobd** - Converts a GEN (impute2) file to a binary dosage data
+  set
+- **bdmerge** - Merges multiple binary dosage data sets into a single
+  data set
+- **getbdinfo** - Creates an R List containing information about a
+  binary dosage data set (required for **getsnp** and **bdapply**)
+- **getvcfinfo** - Creates an R List containing information about a VCF
+  file (required for **vcfapply**)
+- **getgeninfo** - Creates an R List containing information about a GEN
+  file (required for **genapply**)
+- **bdapply** - Applies a function to the data for each SNP in a binary
+  dosage file (requires list returned by **getbdinfo**)
+- **vcfapply** - Applies a function to the data for each SNP in a VCF
+  file (requires list returned by **getvcfinfo**)
+- **genapply** - Applies a function to the data for each SNP in a GEN
+  file (requires list returned by **getgeninfo**)
+- **getsnp** - Obtain genotype Dosages/Genotype Probabilities from a
+  binary dosage file, outputs results to an R list
 
 # Installation
 
@@ -114,6 +174,15 @@ devtools::install_github("https://github.com/USCbiostats/BinaryDosage")
 library(BinaryDosage)
 ```
 
+To install the package with vignettes built, use the `build_vignettes`
+option:
+
+``` r
+devtools::install_github("https://github.com/USCbiostats/BinaryDosage", build_vignettes = TRUE)
+
+library(BinaryDosage)
+```
+
 # Usage
 
 #### General Workflow
@@ -210,11 +279,11 @@ mergebd3 <- tempfile()
 Converting a VCF file into a binary dosage file is simple. The user
 passes the names of the VCF and information files along with the name
 for the binary dosage file to the
-<span style="font-family:Courier">vcftobdlegacy</span> function. There are
-some options available for the
-<span style="font-family:Courier">vcftobdlegacy</span> functions such as using
-gz compressed files vcf files. More information about these options can
-be found using the help files or reading the vignette
+<span style="font-family:Courier">vcftobdlegacy</span> function. There
+are some options available for the
+<span style="font-family:Courier">vcftobdlegacy</span> functions such as
+using gz compressed files vcf files. More information about these
+options can be found using the help files or reading the vignette
 <span style="font-family:Courier">usingvcffiles</span>.
 
 The following commands convert VCF data sets 1a and 1b into the binary