Mercurial > repos > modencode-dcc > bamedit
changeset 3:1cea5a75f998 draft
Uploaded
| author | modencode-dcc |
|---|---|
| date | Fri, 18 Jan 2013 10:53:35 -0500 |
| parents | 1ced8ed78013 |
| children | a4b7eb9c87d9 |
| files | split.sh |
| diffstat | 1 files changed, 25 insertions(+), 0 deletions(-) [+] |
line wrap: on
line diff
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/split.sh Fri Jan 18 10:53:35 2013 -0500 @@ -0,0 +1,25 @@ +#!bin/bash + +#purpose: shell script which performs the split option +#author: Ziru Zhou +#date: October, 2012 + +main() +{ + output1="${1}" + output2="${2}" + input="${3}" + + $(samtools view -H ${input} > tmp) + linecount=$(samtools view ${input} | wc -l) + half=$(((${linecount} + 1) / 2)) + samtools view ${input} | shuf | split -d -l ${half} + + $(cat tmp x00 > x00h) + $(cat tmp x01 > x01h) + samtools view -bSo ${output1} x00h + samtools view -bSo ${output2} x01h + + rm tmp x00h x01h x00 x01 +} +main "${@}"