--- a/wrapper.sh	Tue Jun 07 08:39:08 2016 -0400
+++ b/wrapper.sh	Wed Jun 08 03:54:49 2016 -0400
@@ -77,6 +77,37 @@
 
 Rscript $dir/merge_and_filter.r $PWD/summary.txt $PWD/sequences.txt $PWD/mutationanalysis.txt $PWD/mutationstats.txt $PWD/hotspots.txt $outdir/identified_genes.txt $outdir/merged.txt $outdir/before_unique_filter.txt $outdir/unmatched.txt $method $functionality $unique ${filter_unique} ${class_filter} 2>&1
 
+echo "---------------- creating new IMGT zip ----------------<br />"
+echo "---------------- creating new IMGT zip ----------------<br />" >> $output
+
+mkdir $outdir/new_IMGT
+
+cat `find $PWD/files/ -name "1_*"` > "$outdir/new_IMGT/1_Summary.txt"
+cat `find $PWD/files/ -name "2_*"` > "$outdir/new_IMGT/2_IMGT-gapped-nt-sequences.txt"
+cat `find $PWD/files/ -name "3_*"` > "$outdir/new_IMGT/3_Nt-sequences.txt"
+cat `find $PWD/files/ -name "4_*"` > "$outdir/new_IMGT/4_IMGT-gapped-AA-sequences.txt"
+cat `find $PWD/files/ -name "5_*"` > "$outdir/new_IMGT/5_AA-sequences.txt"
+cat `find $PWD/files/ -name "6_*"` > "$outdir/new_IMGT/6_Junction.txt"
+cat `find $PWD/files/ -name "7_*"` > "$outdir/new_IMGT/7_V-REGION-mutation-and-AA-change-table.txt"
+cat `find $PWD/files/ -name "8_*"` > "$outdir/new_IMGT/8_V-REGION-nt-mutation-statistics.txt"
+cat `find $PWD/files/ -name "9_*"` > "$outdir/new_IMGT/9_V-REGION-AA-change-statistics.txt"
+cat `find $PWD/files/ -name "10_*"` > "$outdir/new_IMGT/10_V-REGION-mutation-hotspots.txt"
+
+Rscript $dir/tmp/igat.r $outdir/new_IMGT/ $outdir/merged.txt 2>&1
+
+
+tmp="$PWD"
+cd $outdir/new_IMGT/ #tar weirdness...
+tar -cJf ../new_IMGT.txz *
+
+cp $dir/tmp/IgAT.xlsm $outdir/new_IMGT/IgAT.xlsm
+
+#tar -cJf ../IgAT.txz *
+zip -r ../IgAT.zip *
+
+cd $tmp
+
+
 echo "---------------- mutation_analysis.r ----------------"
 echo "---------------- mutation_analysis.r ----------------<br />" >> $output
 
@@ -100,6 +131,7 @@
 funcs=(sum mean median)
 
 echo "---------------- sequence_overview.r ----------------"
+echo "---------------- sequence_overview.r ----------------" >> $output
 
 mkdir $outdir/sequence_overview
 
@@ -173,6 +205,9 @@
 echo "<a href='absent_aa_id.txt'>Absant AA locations by id</a><br />" >> $output
 echo "<a href='sequence_overview/index.html'>Sequence Overview</a><br />" >> $output
 echo "<a href='base_overview.html'>Base overview</a><br />" >> $output
+echo "<a href='baseline.pdf'>Baseline PDF</a><br />" >> $output
+echo "<a href='baseline.txt'>Baseline Table</a><br />" >> $output
+echo "<a href='IgAT.zip'>IgAT zip</a><br />" >> $output
 
 echo "---------------- images ----------------"
 
@@ -224,6 +259,8 @@
 
 echo "</html>" >> $output
 
+echo "---------------- baseline ----------------"
+bash $dir/tmp/baseline/wrapper.sh 1 1 1 1 0 0 "25:26:38:55:65:104:-" $outdir/new_IMGT.txz "sample name" "$dir/tmp/baseline/IMGT-reference-seqs-IGHV-2015-11-05.fa" "$outdir/baseline.pdf" "Sequence.ID" "$outdir/baseline.txt"
 
 #optional output for naive
 
@@ -234,6 +271,7 @@
 	echo "---------------- imgt_loader.r ----------------"
 	#python $dir/imgt_loader.py --summ $PWD/summary.txt --aa $PWD/aa.txt --junction $PWD/junction.txt --output $naive_output
 	Rscript --verbose $dir/imgt_loader.r $PWD/summary.txt $PWD/aa.txt $PWD/junction.txt $outdir/loader_output.txt 2>&1
+
 	echo "---------------- naive_output.r ----------------"
 	Rscript $dir/naive_output.r $outdir/loader_output.txt $outdir/merged.txt ${naive_output_ca} ${naive_output_cg} ${naive_output_cm} $outdir/ntoverview.txt $outdir/ntsum.txt 2>&1
 fi