From 8a5e633cef2d5a648c951a4ccc6b24ccaa558c1a Mon Sep 17 00:00:00 2001
From: james-edward-hart <118322559+james-edward-hart@users.noreply.github.com>
Date: Mon, 28 Oct 2024 12:30:44 -0400
Subject: [PATCH 1/3] Update README.md

Edit to GRCh37 human reference genome install code which resolves connection loss and broken pipe issue
---
 README.md | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/README.md b/README.md
index b07a48e..eb4f3c5 100644
--- a/README.md
+++ b/README.md
@@ -332,7 +332,7 @@ export BCFTOOLS_PLUGINS="$HOME/bin"
 
 Install the GRCh37 human genome reference, cytoband and chain file
 ```
-wget -O- ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/technical/reference/human_g1k_v37.fasta.gz | \
+wget --continue 'ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/technical/reference/human_g1k_v37.fasta.gz' -O $HOME/GRCh37/human_g1k_v37.fasta.gz
   gzip -d > $HOME/GRCh37/human_g1k_v37.fasta
 samtools faidx $HOME/GRCh37/human_g1k_v37.fasta
 bwa index $HOME/GRCh37/human_g1k_v37.fasta

From 64e1706d5be4e9c1f8213118b7a8be0dcc5184e8 Mon Sep 17 00:00:00 2001
From: james-edward-hart <118322559+james-edward-hart@users.noreply.github.com>
Date: Mon, 28 Oct 2024 13:24:25 -0400
Subject: [PATCH 2/3] Update README.md

apologies, file name fixed added .gz for the zipped file to be passed to gzip
---
 README.md | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/README.md b/README.md
index eb4f3c5..cbc79dd 100644
--- a/README.md
+++ b/README.md
@@ -333,7 +333,7 @@ export BCFTOOLS_PLUGINS="$HOME/bin"
 Install the GRCh37 human genome reference, cytoband and chain file
 ```
 wget --continue 'ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/technical/reference/human_g1k_v37.fasta.gz' -O $HOME/GRCh37/human_g1k_v37.fasta.gz
-  gzip -d > $HOME/GRCh37/human_g1k_v37.fasta
+  gzip -d > $HOME/GRCh37/human_g1k_v37.fasta.gz
 samtools faidx $HOME/GRCh37/human_g1k_v37.fasta
 bwa index $HOME/GRCh37/human_g1k_v37.fasta
 wget -P $HOME/GRCh37 http://hgdownload.cse.ucsc.edu/goldenPath/hg19/database/cytoBand.txt.gz

From c4b1e77400fa9cdbd7ae0c9db8a4090172c701f5 Mon Sep 17 00:00:00 2001
From: james-edward-hart <118322559+james-edward-hart@users.noreply.github.com>
Date: Mon, 28 Oct 2024 13:57:57 -0400
Subject: [PATCH 3/3] Update README.md

Overwrite tag removed from gzip function
---
 README.md | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/README.md b/README.md
index cbc79dd..e602546 100644
--- a/README.md
+++ b/README.md
@@ -333,7 +333,7 @@ export BCFTOOLS_PLUGINS="$HOME/bin"
 Install the GRCh37 human genome reference, cytoband and chain file
 ```
 wget --continue 'ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/technical/reference/human_g1k_v37.fasta.gz' -O $HOME/GRCh37/human_g1k_v37.fasta.gz
-  gzip -d > $HOME/GRCh37/human_g1k_v37.fasta.gz
+gzip -d $HOME/GRCh37/human_g1k_v37.fasta.gz
 samtools faidx $HOME/GRCh37/human_g1k_v37.fasta
 bwa index $HOME/GRCh37/human_g1k_v37.fasta
 wget -P $HOME/GRCh37 http://hgdownload.cse.ucsc.edu/goldenPath/hg19/database/cytoBand.txt.gz