From 17d7f7cdf97cafc22ea6c979a31cf9fd79f2126e Mon Sep 17 00:00:00 2001
From: daphnehanse11 <128793799+daphnehanse11@users.noreply.github.com>
Date: Fri, 9 Jun 2023 10:46:06 -0400
Subject: [PATCH 01/20] git practice

---
 R/hello.R | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/R/hello.R b/R/hello.R
index aad5c3b..52820b1 100644
--- a/R/hello.R
+++ b/R/hello.R
@@ -1,5 +1,5 @@
 # @
-#
+# I am practicing pushing/commiting with git
 # This is an example function named 'hello'
 # which prints 'Hello, world!'.
 #

From 8d6b1390c0bbdfd6dcbb1736e9ad68645fae4950 Mon Sep 17 00:00:00 2001
From: daphnehanse11 <128793799+daphnehanse11@users.noreply.github.com>
Date: Tue, 13 Jun 2023 10:00:03 -0400
Subject: [PATCH 02/20] Create .Rapp.history

---
 data/.Rapp.history | 3 +++
 1 file changed, 3 insertions(+)
 create mode 100644 data/.Rapp.history

diff --git a/data/.Rapp.history b/data/.Rapp.history
new file mode 100644
index 0000000..d5369f9
--- /dev/null
+++ b/data/.Rapp.history
@@ -0,0 +1,3 @@
+load("/Users/dhansell/Documents/GitHub/balselr/data/example_vcf.rda")
+load("/Users/dhansell/Documents/GitHub/balselr/data/example_vcf.rda")
+print("example_vcf.rda)

From 001be297c5188db7e720093e709a96d06c754784 Mon Sep 17 00:00:00 2001
From: daphnehanse11 <128793799+daphnehanse11@users.noreply.github.com>
Date: Tue, 13 Jun 2023 10:09:32 -0400
Subject: [PATCH 03/20] practice

practice
---
 R/read_vcf.R    | 1 +
 R/vcfpractice.R | 6 ++++++
 2 files changed, 7 insertions(+)
 create mode 100644 R/vcfpractice.R

diff --git a/R/read_vcf.R b/R/read_vcf.R
index f6f22cd..7ab6b6d 100644
--- a/R/read_vcf.R
+++ b/R/read_vcf.R
@@ -22,3 +22,4 @@ read_vcf <- function(x = "inst/example.vcf",
                 inp
         }
 }
+
diff --git a/R/vcfpractice.R b/R/vcfpractice.R
new file mode 100644
index 0000000..2812dbc
--- /dev/null
+++ b/R/vcfpractice.R
@@ -0,0 +1,6 @@
+library("data.table")
+chrom_21b<-read_vcf("~/Documents/ALL.chr21.shapeit2_integrated_v1a.GRCh38.20181129.phased.vcf")
+
+read_vcf(example_vcf)
+
+parse_vcf("~/Documents/ALL.chr21.shapeit2_integrated_v1a.GRCh38.20181129.phased.vcf")

From 29fe23590788010696b0fb14775450a46247d1f4 Mon Sep 17 00:00:00 2001
From: daphnehanse11 <128793799+daphnehanse11@users.noreply.github.com>
Date: Wed, 14 Jun 2023 11:10:18 -0400
Subject: [PATCH 04/20] Update vcfpractice.R

---
 R/vcfpractice.R | 7 ++++---
 1 file changed, 4 insertions(+), 3 deletions(-)

diff --git a/R/vcfpractice.R b/R/vcfpractice.R
index 2812dbc..b45858f 100644
--- a/R/vcfpractice.R
+++ b/R/vcfpractice.R
@@ -1,6 +1,7 @@
 library("data.table")
-chrom_21b<-read_vcf("~/Documents/ALL.chr21.shapeit2_integrated_v1a.GRCh38.20181129.phased.vcf")
 
-read_vcf(example_vcf)
 
-parse_vcf("~/Documents/ALL.chr21.shapeit2_integrated_v1a.GRCh38.20181129.phased.vcf")
+read_vcf("example_vcf")
+
+read_vcf("chrom22.vcf")
+parse_vcf("chrom22.vcf", type = "ncd1")

From 2e18ac8c074fabe6233b423fa42798e99a9e5174 Mon Sep 17 00:00:00 2001
From: daphnehanse11 <128793799+daphnehanse11@users.noreply.github.com>
Date: Wed, 14 Jun 2023 14:08:07 -0400
Subject: [PATCH 05/20] dot removal

---
 R/count_alleles.R | 8 ++++----
 R/read_vcf.R      | 2 +-
 R/split_geno.R    | 2 +-
 R/vcf_ncd1.R      | 6 +++---
 R/vcfpractice.R   | 7 +++++--
 5 files changed, 14 insertions(+), 11 deletions(-)

diff --git a/R/count_alleles.R b/R/count_alleles.R
index ee66be5..95fda27 100644
--- a/R/count_alleles.R
+++ b/R/count_alleles.R
@@ -7,11 +7,11 @@
 #' @param index 1 or 2 or c(1,2). Which alleles to consider.
 #' @examples data.table::data.table(col1="1|1", col2="1|0", col3="0|0") %>%
 #' dplyr::summarise(across(col1:col3, .count_alleles))
-.count_alleles<-function(x, split="|",index=c(1,2), der = F){
-        x<-.split_geno(x = x, split = split, index = index)
+count_alleles<-function(x, split="|",index=c(1,2), der = F){
+        x<-split_geno(x = x, split = split, index = index)
         if(der == T){sum(x, na.rm=T)}else if (der == F){sum(!is.na(x))-sum(x, na.rm=T)}
 }
-.count_nonmissing<-function(x, split="|",index=c(1,2)){
-        x<-.split_geno(x = x, split = split, index = index)
+count_nonmissing<-function(x, split="|",index=c(1,2)){
+        x<-split_geno(x = x, split = split, index = index)
         sum(!is.na(x))
 }
diff --git a/R/read_vcf.R b/R/read_vcf.R
index 7ab6b6d..90a8b17 100644
--- a/R/read_vcf.R
+++ b/R/read_vcf.R
@@ -6,7 +6,7 @@
 #' @return Returns a data.table object
 #' @export
 #'
-#' @examples read_vcf(x="inst/example.vcf", only.bi=T, inds="all")
+#' @examples read_vcf(x="inst/example.vcf", only.bi=T")
 #' @import data.table
 #' @importFrom data.table ":="
 read_vcf <- function(x = "inst/example.vcf",
diff --git a/R/split_geno.R b/R/split_geno.R
index 0f9c83f..db57260 100644
--- a/R/split_geno.R
+++ b/R/split_geno.R
@@ -6,7 +6,7 @@
 #'
 #' @examples split_geno(x = c("0|0","0|1","1|1"))
 #' data.table(col1="1|1", col2="1|0", col3="0|0") %>% dplyr::summarise(across(col1:col3, .split_geno))
-.split_geno <- function(x, split="|",index=c(1,2)) {
+split_geno <- function(x, split="|",index=c(1,2)) {
         #assertthat::assert_that(is.numeric(which.al), err = "Parameter which.al must be numeric")
 
         if(length(x) == 1){
diff --git a/R/vcf_ncd1.R b/R/vcf_ncd1.R
index de31165..cc646b5 100644
--- a/R/vcf_ncd1.R
+++ b/R/vcf_ncd1.R
@@ -13,7 +13,7 @@
 #' @examples inp = read_vcf("inst/example.vcf")
 #' vcf_ncd1(x=inp, outfile=outfile_path("inst/example.vcf"),nind=c(108),
 #' .vcf_ncd1(x=inp, outfile=outfile_path("inst/example.vcf"),nind=108, index.col=10, verbose=T)
-.vcf_ncd1 <- function(x,
+vcf_ncd1 <- function(x,
                      outfile = outfile,
                      nind = nind,
                      index.col = index.col,
@@ -45,11 +45,11 @@
   tableout<-dplyr::bind_cols(tableout,
                              x %>% dplyr::select(all_of(pop0_cols)) %>%
                                 dplyr::rowwise() %>%
-                                dplyr::summarise(across(pop0_cols, .count_alleles)) %>%
+                                dplyr::summarise(across(pop0_cols, count_alleles)) %>%
                                 dplyr::summarise(tx_1 = Reduce(`+`,.)),
                              x %>% dplyr::select(all_of(pop0_cols)) %>%
                                 dplyr::rowwise() %>%
-                                dplyr::summarise(across(pop0_cols, .count_nonmissing)) %>%
+                                dplyr::summarise(across(pop0_cols, count_nonmissing)) %>%
                                 dplyr::summarise(tn_1 = Reduce(`+`,.))
                             ) %>%
                 dplyr::select(CHR, POS, REF, ALT, tx_1, tn_1) %>%
diff --git a/R/vcfpractice.R b/R/vcfpractice.R
index b45858f..39cf016 100644
--- a/R/vcfpractice.R
+++ b/R/vcfpractice.R
@@ -3,5 +3,8 @@ library("data.table")
 
 read_vcf("example_vcf")
 
-read_vcf("chrom22.vcf")
-parse_vcf("chrom22.vcf", type = "ncd1")
+
+read_vcf("/Users/dhansell/Documents/GitHub//chrom22.vcf")
+parsed_vcf22<-parse_vcf("/Users/dhansell/Documents/GitHub//chrom22.vcf", type = "ncd1")
+
+stat22<-ncd1(parsed_vcf22)

From 8f705a410a337e3707eed85c811df56e659048d1 Mon Sep 17 00:00:00 2001
From: daphnehanse11 <128793799+daphnehanse11@users.noreply.github.com>
Date: Wed, 14 Jun 2023 16:09:46 -0400
Subject: [PATCH 06/20] dot removal 2

---
 R/parse_vcf.R   |  2 +-
 R/vcfpractice.R | 10 +++++++++-
 2 files changed, 10 insertions(+), 2 deletions(-)

diff --git a/R/parse_vcf.R b/R/parse_vcf.R
index 91126e6..563cc36 100644
--- a/R/parse_vcf.R
+++ b/R/parse_vcf.R
@@ -98,7 +98,7 @@ parse_vcf <-
         )
     } else if (type == "ncd1") {
       res <-
-        .vcf_ncd1(
+        vcf_ncd1(
           x = inp,
           outfile = outfile,
           nind = nind,
diff --git a/R/vcfpractice.R b/R/vcfpractice.R
index 39cf016..aecdb97 100644
--- a/R/vcfpractice.R
+++ b/R/vcfpractice.R
@@ -6,5 +6,13 @@ read_vcf("example_vcf")
 
 read_vcf("/Users/dhansell/Documents/GitHub//chrom22.vcf")
 parsed_vcf22<-parse_vcf("/Users/dhansell/Documents/GitHub//chrom22.vcf", type = "ncd1")
-
 stat22<-ncd1(parsed_vcf22)
+
+
+
+read_vcf("/Users/dhansell/Documents/GitHub//chrom13.vcf")
+parsed_vcf13<-parse_vcf("/Users/dhansell/Documents/GitHub//chrom13.vcf", type = "ncd1")
+stat13<-ncd1(parsed_vcf13)
+
+devtools::install_github("bitarellolab/balselr")
+library(balselr)

From 03f53fae3fef30b80eb2af4652e4eead8d7893e7 Mon Sep 17 00:00:00 2001
From: daphnehanse11 <128793799+daphnehanse11@users.noreply.github.com>
Date: Thu, 15 Jun 2023 10:37:45 -0400
Subject: [PATCH 07/20] returning dots

---
 R/count_alleles.R | 8 ++++----
 R/ncd1.R          | 1 +
 R/parse_vcf.R     | 2 +-
 R/split_geno.R    | 2 +-
 R/vcf_ncd1.R      | 6 +++---
 5 files changed, 10 insertions(+), 9 deletions(-)

diff --git a/R/count_alleles.R b/R/count_alleles.R
index 95fda27..ee66be5 100644
--- a/R/count_alleles.R
+++ b/R/count_alleles.R
@@ -7,11 +7,11 @@
 #' @param index 1 or 2 or c(1,2). Which alleles to consider.
 #' @examples data.table::data.table(col1="1|1", col2="1|0", col3="0|0") %>%
 #' dplyr::summarise(across(col1:col3, .count_alleles))
-count_alleles<-function(x, split="|",index=c(1,2), der = F){
-        x<-split_geno(x = x, split = split, index = index)
+.count_alleles<-function(x, split="|",index=c(1,2), der = F){
+        x<-.split_geno(x = x, split = split, index = index)
         if(der == T){sum(x, na.rm=T)}else if (der == F){sum(!is.na(x))-sum(x, na.rm=T)}
 }
-count_nonmissing<-function(x, split="|",index=c(1,2)){
-        x<-split_geno(x = x, split = split, index = index)
+.count_nonmissing<-function(x, split="|",index=c(1,2)){
+        x<-.split_geno(x = x, split = split, index = index)
         sum(!is.na(x))
 }
diff --git a/R/ncd1.R b/R/ncd1.R
index c7ad866..fefea79 100644
--- a/R/ncd1.R
+++ b/R/ncd1.R
@@ -28,6 +28,7 @@
 ncd1 <- function(x = x,
                  tf = 0.5,
                  fold = T,
+
                  w = 3000,
                  by.snp = TRUE,
                  mid = FALSE,
diff --git a/R/parse_vcf.R b/R/parse_vcf.R
index 563cc36..91126e6 100644
--- a/R/parse_vcf.R
+++ b/R/parse_vcf.R
@@ -98,7 +98,7 @@ parse_vcf <-
         )
     } else if (type == "ncd1") {
       res <-
-        vcf_ncd1(
+        .vcf_ncd1(
           x = inp,
           outfile = outfile,
           nind = nind,
diff --git a/R/split_geno.R b/R/split_geno.R
index db57260..0f9c83f 100644
--- a/R/split_geno.R
+++ b/R/split_geno.R
@@ -6,7 +6,7 @@
 #'
 #' @examples split_geno(x = c("0|0","0|1","1|1"))
 #' data.table(col1="1|1", col2="1|0", col3="0|0") %>% dplyr::summarise(across(col1:col3, .split_geno))
-split_geno <- function(x, split="|",index=c(1,2)) {
+.split_geno <- function(x, split="|",index=c(1,2)) {
         #assertthat::assert_that(is.numeric(which.al), err = "Parameter which.al must be numeric")
 
         if(length(x) == 1){
diff --git a/R/vcf_ncd1.R b/R/vcf_ncd1.R
index cc646b5..de31165 100644
--- a/R/vcf_ncd1.R
+++ b/R/vcf_ncd1.R
@@ -13,7 +13,7 @@
 #' @examples inp = read_vcf("inst/example.vcf")
 #' vcf_ncd1(x=inp, outfile=outfile_path("inst/example.vcf"),nind=c(108),
 #' .vcf_ncd1(x=inp, outfile=outfile_path("inst/example.vcf"),nind=108, index.col=10, verbose=T)
-vcf_ncd1 <- function(x,
+.vcf_ncd1 <- function(x,
                      outfile = outfile,
                      nind = nind,
                      index.col = index.col,
@@ -45,11 +45,11 @@ vcf_ncd1 <- function(x,
   tableout<-dplyr::bind_cols(tableout,
                              x %>% dplyr::select(all_of(pop0_cols)) %>%
                                 dplyr::rowwise() %>%
-                                dplyr::summarise(across(pop0_cols, count_alleles)) %>%
+                                dplyr::summarise(across(pop0_cols, .count_alleles)) %>%
                                 dplyr::summarise(tx_1 = Reduce(`+`,.)),
                              x %>% dplyr::select(all_of(pop0_cols)) %>%
                                 dplyr::rowwise() %>%
-                                dplyr::summarise(across(pop0_cols, count_nonmissing)) %>%
+                                dplyr::summarise(across(pop0_cols, .count_nonmissing)) %>%
                                 dplyr::summarise(tn_1 = Reduce(`+`,.))
                             ) %>%
                 dplyr::select(CHR, POS, REF, ALT, tx_1, tn_1) %>%

From 9d23726eb6834ec7ae874c420c2a339495dce3e7 Mon Sep 17 00:00:00 2001
From: daphnehanse11 <128793799+daphnehanse11@users.noreply.github.com>
Date: Fri, 16 Jun 2023 12:42:50 -0400
Subject: [PATCH 08/20] correcting user error

---
 R/parse_vcf.R | 10 ++++++----
 R/read_vcf.R  |  1 -
 2 files changed, 6 insertions(+), 5 deletions(-)

diff --git a/R/parse_vcf.R b/R/parse_vcf.R
index 91126e6..2499e8d 100644
--- a/R/parse_vcf.R
+++ b/R/parse_vcf.R
@@ -22,9 +22,9 @@
 parse_vcf <-
   function(infile = "*.vcf",
            outfile = NULL,
-           n0=108,
-           n1=NULL,
-           type = "ncd2",
+           n0= NULL,
+           n1= NULL,
+           type = NULL,
            fold = T,
            intern = T,
            verbose = T) {
@@ -32,7 +32,9 @@ parse_vcf <-
     assertthat::assert_that(file.exists(infile),
       msg = glue::glue("VCF file {infile} does not exist.\n")
     )
-    type <- tolower(type)
+    assertthat::assert_that(is.numeric(n0)
+      )
+     type <- tolower(type)
     # Index No. of the individual to use as ``ancestral'' sequence
     if (fold == F & type == "ncd2") {
             outseq <- (index.col) + (sum(nind) - 1)
diff --git a/R/read_vcf.R b/R/read_vcf.R
index 90a8b17..773eb7d 100644
--- a/R/read_vcf.R
+++ b/R/read_vcf.R
@@ -22,4 +22,3 @@ read_vcf <- function(x = "inst/example.vcf",
                 inp
         }
 }
-

From 916b6d99a9a6438af69a9f4d46d985fe0057e5f6 Mon Sep 17 00:00:00 2001
From: daphnehanse11 <128793799+daphnehanse11@users.noreply.github.com>
Date: Fri, 16 Jun 2023 16:41:58 -0400
Subject: [PATCH 09/20] Update read_vcf.R

---
 R/read_vcf.R | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/R/read_vcf.R b/R/read_vcf.R
index 7ab6b6d..90a8b17 100644
--- a/R/read_vcf.R
+++ b/R/read_vcf.R
@@ -6,7 +6,7 @@
 #' @return Returns a data.table object
 #' @export
 #'
-#' @examples read_vcf(x="inst/example.vcf", only.bi=T, inds="all")
+#' @examples read_vcf(x="inst/example.vcf", only.bi=T")
 #' @import data.table
 #' @importFrom data.table ":="
 read_vcf <- function(x = "inst/example.vcf",

From b20552f34e5eb6517cace072d33c3e2b8bd8721b Mon Sep 17 00:00:00 2001
From: daphnehanse11 <128793799+daphnehanse11@users.noreply.github.com>
Date: Tue, 20 Jun 2023 11:05:05 -0400
Subject: [PATCH 10/20] correcting user error

---
 R/parse_vcf.R | 23 ++++++++++++++++++++---
 1 file changed, 20 insertions(+), 3 deletions(-)

diff --git a/R/parse_vcf.R b/R/parse_vcf.R
index 2499e8d..34b4721 100644
--- a/R/parse_vcf.R
+++ b/R/parse_vcf.R
@@ -34,9 +34,26 @@ parse_vcf <-
     )
     assertthat::assert_that(is.numeric(n0)
       )
-     type <- tolower(type)
-    # Index No. of the individual to use as ``ancestral'' sequence
-    if (fold == F & type == "ncd2") {
+        format_type <- function(type) {
+             incorrect_types_ncd1 <- c("ncd1", "ned1", "ncd_1", "ned_1")
+             incorrect_types_ncd2 <- c("ncd2", "ned2", "ncd_2", "ned_2")
+
+             type <- tolower(type)
+             if (type %in% incorrect_types_ncd1) {
+                     type <- "ncd1"
+             } else if (type %in% incorrect_types_ncd2) {
+                     type <- "ncd2"
+             }
+
+             return(type)
+
+        }
+        if (is.null(type)) {
+                print("You must choose either 'ncd1' or 'ncd2'")
+                return(NULL)
+        }
+        # Index No. of the individual to use as ``ancestral'' sequence
+        if (fold == F & type == "ncd2") {
             outseq <- (index.col) + (sum(nind) - 1)
             if (verbose == T) {
                     cat(

From ec1a25994f5f6b2167becd3a27576e86e5c59b8e Mon Sep 17 00:00:00 2001
From: daphnehanse11 <128793799+daphnehanse11@users.noreply.github.com>
Date: Wed, 21 Jun 2023 12:01:41 -0400
Subject: [PATCH 11/20] Update vcfpractice.R

---
 R/vcfpractice.R | 20 ++++++++++----------
 1 file changed, 10 insertions(+), 10 deletions(-)

diff --git a/R/vcfpractice.R b/R/vcfpractice.R
index aecdb97..5726fd4 100644
--- a/R/vcfpractice.R
+++ b/R/vcfpractice.R
@@ -1,18 +1,18 @@
-library("data.table")
+#library("data.table")
 
 
-read_vcf("example_vcf")
+#read_vcf("example_vcf")
 
 
-read_vcf("/Users/dhansell/Documents/GitHub//chrom22.vcf")
-parsed_vcf22<-parse_vcf("/Users/dhansell/Documents/GitHub//chrom22.vcf", type = "ncd1")
-stat22<-ncd1(parsed_vcf22)
+#read_vcf("/Users/dhansell/Documents/GitHub//chrom22.vcf")
+#parsed_vcf22<-parse_vcf("/Users/dhansell/Documents/GitHub//chrom22.vcf", type = "ncd1")
+#stat22<-ncd1(parsed_vcf22)
 
 
 
-read_vcf("/Users/dhansell/Documents/GitHub//chrom13.vcf")
-parsed_vcf13<-parse_vcf("/Users/dhansell/Documents/GitHub//chrom13.vcf", type = "ncd1")
-stat13<-ncd1(parsed_vcf13)
+#read_vcf("/Users/dhansell/Documents/GitHub//chrom13.vcf")
+#parsed_vcf13<-parse_vcf("/Users/dhansell/Documents/GitHub//chrom13.vcf", type = "ncd1")
+#stat13<-ncd1(parsed_vcf13)
 
-devtools::install_github("bitarellolab/balselr")
-library(balselr)
+#devtools::install_github("bitarellolab/balselr")
+#library(balselr)

From 0b57a6c67defaadfbfc69eb9ec2e3f6a956e96c5 Mon Sep 17 00:00:00 2001
From: daphnehanse11 <128793799+daphnehanse11@users.noreply.github.com>
Date: Wed, 21 Jun 2023 15:46:05 -0400
Subject: [PATCH 12/20] working on tests

---
 tests/test-readvcf.R | 0
 tests/testthat.R     | 5 -----
 2 files changed, 5 deletions(-)
 create mode 100644 tests/test-readvcf.R

diff --git a/tests/test-readvcf.R b/tests/test-readvcf.R
new file mode 100644
index 0000000..e69de29
diff --git a/tests/testthat.R b/tests/testthat.R
index 29ea3ab..a621d1c 100644
--- a/tests/testthat.R
+++ b/tests/testthat.R
@@ -5,8 +5,3 @@
 # Learn more about the roles of various files in:
 # * https://r-pkgs.org/tests.html
 # * https://testthat.r-lib.org/reference/test_package.html#special-files
-
-library(testthat)
-library(balselr)
-
-test_check("balselr")

From b0297ba929a629fb653ba2b7efc2aca299ce9f71 Mon Sep 17 00:00:00 2001
From: daphnehanse11 <128793799+daphnehanse11@users.noreply.github.com>
Date: Thu, 22 Jun 2023 10:15:54 -0400
Subject: [PATCH 13/20] Update test-readvcf.R

---
 tests/test-readvcf.R | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/tests/test-readvcf.R b/tests/test-readvcf.R
index e69de29..cd0beb7 100644
--- a/tests/test-readvcf.R
+++ b/tests/test-readvcf.R
@@ -0,0 +1,2 @@
+#the output should be a data.table
+#the output should

From 79fc2e3e17f705cc4bc54b4923141b1be44290bd Mon Sep 17 00:00:00 2001
From: daphnehanse11 <128793799+daphnehanse11@users.noreply.github.com>
Date: Thu, 22 Jun 2023 12:31:03 -0400
Subject: [PATCH 14/20] writing tests

---
 man/read_vcf.Rd      | 3 ---
 tests/test-readvcf.R | 8 +++++++-
 2 files changed, 7 insertions(+), 4 deletions(-)

diff --git a/man/read_vcf.Rd b/man/read_vcf.Rd
index 1356f73..f12cc87 100644
--- a/man/read_vcf.Rd
+++ b/man/read_vcf.Rd
@@ -18,6 +18,3 @@ Returns a data.table object
 \description{
 Read vcf
 }
-\examples{
-read_vcf(x="inst/example.vcf", only.bi=T, inds="all")
-}
diff --git a/tests/test-readvcf.R b/tests/test-readvcf.R
index cd0beb7..b07d954 100644
--- a/tests/test-readvcf.R
+++ b/tests/test-readvcf.R
@@ -1,2 +1,8 @@
 #the output should be a data.table
-#the output should
+
+testthat::test_that("output is a data table", {
+        readinvcf <-  read_vcf(x="inst/example.vcf")
+        testthat::expect_type(readinvcf, "data.frame")
+})
+
+

From 165b56496a36a7415abbfd33ff09477ef51d481c Mon Sep 17 00:00:00 2001
From: daphnehanse11 <128793799+daphnehanse11@users.noreply.github.com>
Date: Thu, 22 Jun 2023 12:41:04 -0400
Subject: [PATCH 15/20] more tests

---
 tests/test-readvcf.R | 7 +++++--
 1 file changed, 5 insertions(+), 2 deletions(-)

diff --git a/tests/test-readvcf.R b/tests/test-readvcf.R
index b07d954..d2610e8 100644
--- a/tests/test-readvcf.R
+++ b/tests/test-readvcf.R
@@ -1,8 +1,11 @@
 #the output should be a data.table
 
 testthat::test_that("output is a data table", {
-        readinvcf <-  read_vcf(x="inst/example.vcf")
+        readinvcf <-  read_vcf(x="inst/example.vcf", only.bi = TRUE)
         testthat::expect_type(readinvcf, "data.frame")
 })
 
-
+testthat::test_that("read_vcf correctly renames column", {
+        readinvcf <- read_vcf(vcf_file_path, only.bi = TRUE)
+        testthat::expect_true("CHR" %in% colnames(readinvcf))
+})

From d611326d74ac6680792e1102db41de44a031f4e4 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?B=C3=A1rbara=20Bitarello?= <barbarabitarello@gmail.com>
Date: Thu, 18 Apr 2024 12:03:33 -0400
Subject: [PATCH 16/20] Delete hello.R

---
 R/hello.R | 18 ------------------
 1 file changed, 18 deletions(-)
 delete mode 100644 R/hello.R

diff --git a/R/hello.R b/R/hello.R
deleted file mode 100644
index 52820b1..0000000
--- a/R/hello.R
+++ /dev/null
@@ -1,18 +0,0 @@
-# @
-# I am practicing pushing/commiting with git
-# This is an example function named 'hello'
-# which prints 'Hello, world!'.
-#
-# You can learn more about package authoring with RStudio at:
-#
-#   v
-#
-# Some useful keyboard shortcuts for package authoring:
-#
-#   Install Package:           'Cmd + Shift + B'
-#   Check Package:             'Cmd + Shift + E'
-#   Test Package:              'Cmd + Shift + T'
-#' @export
-hello <- function() {
-  print("Hello, world!")
-}

From 122f4e6fcb0a291df008ca88814592abfb74641b Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?B=C3=A1rbara=20Bitarello?= <barbarabitarello@gmail.com>
Date: Thu, 18 Apr 2024 12:33:03 -0400
Subject: [PATCH 17/20] asfdasfs

---
 R/vcfpractice.R                 |  18 -
 example_parse_ncd2.out_ncd2.out | 839 --------------------------------
 2 files changed, 857 deletions(-)
 delete mode 100644 R/vcfpractice.R
 delete mode 100644 example_parse_ncd2.out_ncd2.out

diff --git a/R/vcfpractice.R b/R/vcfpractice.R
deleted file mode 100644
index 5726fd4..0000000
--- a/R/vcfpractice.R
+++ /dev/null
@@ -1,18 +0,0 @@
-#library("data.table")
-
-
-#read_vcf("example_vcf")
-
-
-#read_vcf("/Users/dhansell/Documents/GitHub//chrom22.vcf")
-#parsed_vcf22<-parse_vcf("/Users/dhansell/Documents/GitHub//chrom22.vcf", type = "ncd1")
-#stat22<-ncd1(parsed_vcf22)
-
-
-
-#read_vcf("/Users/dhansell/Documents/GitHub//chrom13.vcf")
-#parsed_vcf13<-parse_vcf("/Users/dhansell/Documents/GitHub//chrom13.vcf", type = "ncd1")
-#stat13<-ncd1(parsed_vcf13)
-
-#devtools::install_github("bitarellolab/balselr")
-#library(balselr)
diff --git a/example_parse_ncd2.out_ncd2.out b/example_parse_ncd2.out_ncd2.out
deleted file mode 100644
index dcafcbb..0000000
--- a/example_parse_ncd2.out_ncd2.out
+++ /dev/null
@@ -1,839 +0,0 @@
-CHR	POS	REF	ALT	tx_1	tn_1	tx_2	tn_2
-1	92	A	C	0	216	2	2
-1	177	C	A	0	216	2	2
-1	283	T	C	216	216	2	2
-1	289	C	G	216	216	0	2
-1	327	G	T	216	216	1	2
-1	331	T	C	216	216	2	2
-1	332	C	A	216	216	2	2
-1	368	A	G	216	216	2	2
-1	382	A	C	216	216	2	2
-1	394	A	G	0	216	2	2
-1	398	C	T	215	216	2	2
-1	441	C	G	216	216	2	2
-1	471	C	A	216	216	1	2
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-1	522	A	G	216	216	2	2
-1	568	C	A	0	216	2	2
-1	585	T	C	216	216	0	2
-1	627	A	T	83	216	2	2
-1	669	C	T	216	216	0	2
-1	674	T	A	216	216	2	2
-1	687	C	G	216	216	2	2
-1	706	T	G	216	216	2	2
-1	719	C	T	0	216	2	2
-1	743	A	C	216	216	2	2
-1	835	G	A	216	216	2	2
-1	868	C	G	0	216	2	2
-1	904	A	T	216	216	1	2
-1	956	C	G	149	216	2	2
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-1	1155	A	G	211	216	2	2
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-1	1363	T	G	0	216	0	2
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-1	1441	T	A	212	216	2	2
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-1	28439	T	A	214	216	2	2
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-1	28465	G	A	216	216	0	2
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From ba44052bcf25630e7a2f429d916fc4d123a8ff5c Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?B=C3=A1rbara=20Bitarello?= <barbarabitarello@gmail.com>
Date: Thu, 18 Apr 2024 12:44:13 -0400
Subject: [PATCH 18/20] asdasa

---
 DESCRIPTION     |  3 ++-
 NAMESPACE       |  1 -
 R/read_vcf.R    | 22 +++++++---------------
 man/read_vcf.Rd | 10 +++++-----
 4 files changed, 14 insertions(+), 22 deletions(-)

diff --git a/DESCRIPTION b/DESCRIPTION
index 2b9108f..891b3f9 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -8,7 +8,7 @@ Description: Produce input files for different balancing selection programs/test
 License: MIT + file LICENSE
 Encoding: UTF-8
 Roxygen: list(markdown = TRUE)
-RoxygenNote: 7.2.3
+RoxygenNote: 7.3.1
 LazyData: true
 Imports: 
     assertthat,
@@ -23,3 +23,4 @@ Imports:
     tictoc
 Depends: 
     R (>= 2.10)
+Config/testthat/edition: 3
diff --git a/NAMESPACE b/NAMESPACE
index 64aed57..94c74e2 100644
--- a/NAMESPACE
+++ b/NAMESPACE
@@ -1,7 +1,6 @@
 # Generated by roxygen2: do not edit by hand
 
 export("%>%")
-export(hello)
 export(ncd1)
 export(ncd2)
 export(outfile_path)
diff --git a/R/read_vcf.R b/R/read_vcf.R
index 90a8b17..797953c 100644
--- a/R/read_vcf.R
+++ b/R/read_vcf.R
@@ -1,25 +1,17 @@
 #' Read vcf
 #'
 #' @param x The path and name of a vcf file
-#' @param only.bi Logical. If TRUE, only bi-allelic SNP positions from VCF file
-#' are kept.
-#' @return Returns a data.table object
+#' @return Returns a data.table object containing only SNPs
 #' @export
 #'
-#' @examples read_vcf(x="inst/example.vcf", only.bi=T")
+#' @examples read_vcf(x=system.file(package="balselr", "example.vcf"))
 #' @import data.table
 #' @importFrom data.table ":="
-read_vcf <- function(x = "inst/example.vcf",
-                     only.bi = T) {
-        REF <- ALT <- x2 <- NULL
+#'
+read_vcf <- function(x = "inst/example.vcf") {
         inp <- data.table::fread(x, skip = "##", header = T)
         data.table::setnames(inp, "#CHROM", "CHR")
-        if (only.bi == T) {
-                inp <-
-                        inp[REF %in% c("A", "C", "T", "G")][ALT %in% c("A", "C", "T", "G")]
-                inp
-        } else {
-                inp
-        }
+        #inp <-
+        inp[REF %in% c("A", "C", "T", "G")][ALT %in% c("A", "C", "T", "G")]
+        #return(inp)
 }
-
diff --git a/man/read_vcf.Rd b/man/read_vcf.Rd
index f12cc87..5bb927f 100644
--- a/man/read_vcf.Rd
+++ b/man/read_vcf.Rd
@@ -4,17 +4,17 @@
 \alias{read_vcf}
 \title{Read vcf}
 \usage{
-read_vcf(x = "inst/example.vcf", only.bi = T)
+read_vcf(x = "inst/example.vcf")
 }
 \arguments{
 \item{x}{The path and name of a vcf file}
-
-\item{only.bi}{Logical. If TRUE, only bi-allelic SNP positions from VCF file
-are kept.}
 }
 \value{
-Returns a data.table object
+Returns a data.table object containing only SNPs
 }
 \description{
 Read vcf
 }
+\examples{
+read_vcf(x=system.file(package="balselr", "example.vcf"))
+}

From 0f5daa724225c3b4be62148ed93e5fcc19d8e53f Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?B=C3=A1rbara=20Bitarello?= <barbarabitarello@gmail.com>
Date: Thu, 18 Apr 2024 12:55:54 -0400
Subject: [PATCH 19/20] push to master

Push to master
---
 data/.Rapp.history   |  3 ---
 man/hello.Rd         | 12 ------------
 tests/test-readvcf.R | 11 -----------
 3 files changed, 26 deletions(-)
 delete mode 100644 data/.Rapp.history
 delete mode 100644 man/hello.Rd
 delete mode 100644 tests/test-readvcf.R

diff --git a/data/.Rapp.history b/data/.Rapp.history
deleted file mode 100644
index d5369f9..0000000
--- a/data/.Rapp.history
+++ /dev/null
@@ -1,3 +0,0 @@
-load("/Users/dhansell/Documents/GitHub/balselr/data/example_vcf.rda")
-load("/Users/dhansell/Documents/GitHub/balselr/data/example_vcf.rda")
-print("example_vcf.rda)
diff --git a/man/hello.Rd b/man/hello.Rd
deleted file mode 100644
index 0fa7c4b..0000000
--- a/man/hello.Rd
+++ /dev/null
@@ -1,12 +0,0 @@
-\name{hello}
-\alias{hello}
-\title{Hello, World!}
-\usage{
-hello()
-}
-\description{
-Prints 'Hello, world!'.
-}
-\examples{
-hello()
-}
diff --git a/tests/test-readvcf.R b/tests/test-readvcf.R
deleted file mode 100644
index d2610e8..0000000
--- a/tests/test-readvcf.R
+++ /dev/null
@@ -1,11 +0,0 @@
-#the output should be a data.table
-
-testthat::test_that("output is a data table", {
-        readinvcf <-  read_vcf(x="inst/example.vcf", only.bi = TRUE)
-        testthat::expect_type(readinvcf, "data.frame")
-})
-
-testthat::test_that("read_vcf correctly renames column", {
-        readinvcf <- read_vcf(vcf_file_path, only.bi = TRUE)
-        testthat::expect_true("CHR" %in% colnames(readinvcf))
-})

From f9aebb2a567ec7b59ca2cc767300721c39a5528e Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?B=C3=A1rbara=20Bitarello?= <barbarabitarello@gmail.com>
Date: Thu, 18 Apr 2024 12:56:28 -0400
Subject: [PATCH 20/20] Update DATASET.R

---
 data-raw/DATASET.R | 3 ---
 1 file changed, 3 deletions(-)

diff --git a/data-raw/DATASET.R b/data-raw/DATASET.R
index 6514a94..e69de29 100644
--- a/data-raw/DATASET.R
+++ b/data-raw/DATASET.R
@@ -1,3 +0,0 @@
-## code to prepare `DATASET` dataset goes here
-
-usethis::use_data(DATASET, overwrite = TRUE)