# HG changeset patch
# User davidvanzessen
# Date 1614249152 0
# Node ID a103134ee6e06db61f0754cbc531867ac5a2aa8d
# Parent  b6f9a640e0983ffaa444d41c48f88f87aceaa0b2
Uploaded

diff -r b6f9a640e098 -r a103134ee6e0 .gitattributes
--- a/.gitattributes	Fri Feb 19 15:10:54 2021 +0000
+++ b/.gitattributes	Thu Feb 25 10:32:32 2021 +0000
@@ -1,2 +1,4 @@
 # Auto detect text files and perform LF normalization
 * text=auto
+# Convert to LF line endings on checkout.
+*.sh text eol=lf
\ No newline at end of file
diff -r b6f9a640e098 -r a103134ee6e0 change_o/define_clones.sh
--- a/change_o/define_clones.sh	Fri Feb 19 15:10:54 2021 +0000
+++ b/change_o/define_clones.sh	Thu Feb 25 10:32:32 2021 +0000
@@ -1,39 +1,40 @@
-#!/bin/bash
-dir="$(cd "$(dirname "$0")" && pwd)"
-
-#define_clones.sh $input $noparse $scores $regions $out_file
-
-type=$1
-input=$2
-
-mkdir -p $PWD/outdir
-
-cp $input $PWD/input.tab #file has to have a ".tab" extension
-
-if [ "bygroup" == "$type" ] ; then	
-	mode=$3
-	act=$4
-	model=$5
-	norm=$6
-	sym=$7
-	link=$8
-	dist=$9
-	output=${10}
-	output2=${11}
-	
-	DefineClones.py -d $PWD/input.tab --nproc 4 --outdir $PWD/outdir --outname output --mode $mode --act $act --model $model --dist $dist --norm $norm --sym $sym --link $link
-	
-	Rscript $dir/define_clones.r $PWD/outdir/output_clone-pass.tab $output2 2>&1
-else
-	method=$3
-	output=$4
-	output2=$5
-	
-	DefineClones.py hclust -d $PWD/input.tab --nproc 4 --outdir $PWD/outdir --outname output --method $method
-	
-	Rscript $dir/define_clones.r $PWD/outdir/output_clone-pass.tab $output2 2>&1
-fi
-
-cp $PWD/outdir/output_clone-pass.tab $output
-
-rm -rf $PWD/outdir/
+#!/bin/bash
+# something to make it commit, with unix line ends
+dir="$(cd "$(dirname "$0")" && pwd)"
+
+#define_clones.sh $input $noparse $scores $regions $out_file
+
+type=$1
+input=$2
+
+mkdir -p $PWD/outdir
+
+cp $input $PWD/input.tab #file has to have a ".tab" extension
+
+if [ "bygroup" == "$type" ] ; then	
+	mode=$3
+	act=$4
+	model=$5
+	norm=$6
+	sym=$7
+	link=$8
+	dist=$9
+	output=${10}
+	output2=${11}
+	
+	DefineClones.py -d $PWD/input.tab --nproc 4 --outdir $PWD/outdir --outname output --mode $mode --act $act --model $model --dist $dist --norm $norm --sym $sym --link $link
+	
+	Rscript $dir/define_clones.r $PWD/outdir/output_clone-pass.tab $output2 2>&1
+else
+	method=$3
+	output=$4
+	output2=$5
+	
+	DefineClones.py hclust -d $PWD/input.tab --nproc 4 --outdir $PWD/outdir --outname output --method $method
+	
+	Rscript $dir/define_clones.r $PWD/outdir/output_clone-pass.tab $output2 2>&1
+fi
+
+cp $PWD/outdir/output_clone-pass.tab $output
+
+rm -rf $PWD/outdir/
diff -r b6f9a640e098 -r a103134ee6e0 change_o/lr.txt
diff -r b6f9a640e098 -r a103134ee6e0 change_o/makedb.sh
--- a/change_o/makedb.sh	Fri Feb 19 15:10:54 2021 +0000
+++ b/change_o/makedb.sh	Thu Feb 25 10:32:32 2021 +0000
@@ -1,36 +1,36 @@
-#!/bin/bash
-dir="$(cd "$(dirname "$0")" && pwd)"
-
-input=$1
-noparse=$2
-scores=$3
-regions=$4
-output=$5
-
-if [ "true" == "$noparse" ] ; then
-	noparse="--noparse"
-else
-	noparse=""
-fi
-
-if [ "true" == "$scores" ] ; then
-	scores="--scores"
-else
-	scores=""
-fi
-
-if [ "true" == "$regions" ] ; then
-	regions="--regions"
-else
-	regions=""
-fi
-
-mkdir $PWD/outdir
-
-echo "makedb: $PWD/outdir"
-
-MakeDb.py imgt -i $input --outdir $PWD/outdir --outname output $noparse $scores $regions
-
-mv $PWD/outdir/output_db-pass.tab $output
-
-rm -rf $PWD/outdir/
+#!/bin/bash
+dir="$(cd "$(dirname "$0")" && pwd)"
+
+input=$1
+noparse=$2
+scores=$3
+regions=$4
+output=$5
+
+if [ "true" == "$noparse" ] ; then
+	noparse="--noparse"
+else
+	noparse=""
+fi
+
+if [ "true" == "$scores" ] ; then
+	scores="--scores"
+else
+	scores=""
+fi
+
+if [ "true" == "$regions" ] ; then
+	regions="--regions"
+else
+	regions=""
+fi
+
+mkdir $PWD/outdir
+
+echo "makedb: $PWD/outdir"
+
+MakeDb.py imgt -i $input --outdir $PWD/outdir --outname output $noparse $scores $regions
+
+mv $PWD/outdir/output_db-pass.tab $output
+
+rm -rf $PWD/outdir/