--- a/wrapper.sh	Thu Jun 16 05:05:47 2016 -0400
+++ b/wrapper.sh	Thu Jun 16 10:01:54 2016 -0400
@@ -93,21 +93,44 @@
 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
+mkdir $outdir/new_IMGT_ca
+cp $outdir/new_IMGT/* $outdir/new_IMGT_ca
+
+mkdir $outdir/new_IMGT_cg
+cp $outdir/new_IMGT/* $outdir/new_IMGT_cg
+
+mkdir $outdir/new_IMGT_cm
+cp $outdir/new_IMGT/* $outdir/new_IMGT_cm
+
+Rscript $dir/tmp/igat.r $outdir/new_IMGT/ $outdir/merged.txt "-" 2>&1
+Rscript $dir/tmp/igat.r $outdir/new_IMGT_ca/ $outdir/merged.txt "ca "2>&1
+Rscript $dir/tmp/igat.r $outdir/new_IMGT_cg/ $outdir/merged.txt "cg "2>&1
+Rscript $dir/tmp/igat.r $outdir/new_IMGT_cm/ $outdir/merged.txt "cm "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 $outdir/new_IMGT_ca/
+tar -cJf ../new_IMGT_ca.txz *
+cp $dir/tmp/IgAT.xlsm $outdir/new_IMGT_ca/IgAT.xlsm
+zip -r ../IgAT_ca.zip *
+
+cd $outdir/new_IMGT_cg/
+tar -cJf ../new_IMGT_cg.txz *
+cp $dir/tmp/IgAT.xlsm $outdir/new_IMGT_cg/IgAT.xlsm
+zip -r ../IgAT_cg.zip *
+
+cd $outdir/new_IMGT_cm/
+tar -cJf ../new_IMGT_cm.txz *
+cp $dir/tmp/IgAT.xlsm $outdir/new_IMGT_cm/IgAT.xlsm
+zip -r ../IgAT_cm.zip *
+
 cd $tmp
 
-
 echo "---------------- mutation_analysis.r ----------------"
 echo "---------------- mutation_analysis.r ----------------<br />" >> $output
 
@@ -136,7 +159,7 @@
 mkdir $outdir/sequence_overview
 
 #Rscript $dir/sequence_overview.r $outdir/identified_genes.txt $PWD/sequences.txt $outdir/merged.txt $outdir/sequence_overview $classes $outdir/hotspot_analysis_sum.txt 2>&1
-Rscript $dir/sequence_overview.r $outdir/before_unique_filter.txt $outdir/merged.txt $outdir/sequence_overview $classes $outdir/hotspot_analysis_sum.txt 2>&1
+Rscript $dir/sequence_overview.r $outdir/before_unique_filter.txt $outdir/sequence_overview $classes $outdir/hotspot_analysis_sum.txt 2>&1
 
 echo "<table border='1'>" > $outdir/base_overview.html
 
@@ -207,7 +230,21 @@
 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='baseline_ca.pdf'>Baseline ca PDF</a><br />" >> $output
+echo "<a href='baseline_ca.txt'>Baseline ca Table</a><br />" >> $output
+echo "<a href='baseline_cg.pdf'>Baseline cg PDF</a><br />" >> $output
+echo "<a href='baseline_cg.txt'>Baseline cg Table</a><br />" >> $output
+echo "<a href='baseline_cm.pdf'>Baseline cm PDF</a><br />" >> $output
+echo "<a href='baseline_cm.txt'>Baseline cm Table</a><br />" >> $output
 echo "<a href='IgAT.zip'>IgAT zip</a><br />" >> $output
+echo "<a href='IgAT_ca.zip'>IgAT ca zip</a><br />" >> $output
+echo "<a href='IgAT_cg.zip'>IgAT cg zip</a><br />" >> $output
+echo "<a href='IgAT_cm.zip'>IgAT cm zip</a><br />" >> $output
+echo "<a href='new_IMGT.txz'>Filtered IMGT zip</a><br />" >> $output
+echo "<a href='new_IMGT_ca.txz'>Filtered ca IMGT zip</a><br />" >> $output
+echo "<a href='new_IMGT_cg.txz'>Filtered cg IMGT zip</a><br />" >> $output
+echo "<a href='new_IMGT_cm.txz'>Filtered cm IMGT zip</a><br />" >> $output
+
 
 echo "---------------- images ----------------"
 
@@ -260,7 +297,10 @@
 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"
+bash $dir/tmp/baseline/wrapper.sh 1 1 1 1 0 0 "25:26:38:55:65:104:-" $outdir/new_IMGT.txz "ca_cg_cm" "$dir/tmp/baseline/IMGT-reference-seqs-IGHV-2015-11-05.fa" "$outdir/baseline.pdf" "Sequence.ID" "$outdir/baseline.txt"
+bash $dir/tmp/baseline/wrapper.sh 1 1 1 1 0 0 "25:26:38:55:65:104:-" $outdir/new_IMGT_ca.txz "ca" "$dir/tmp/baseline/IMGT-reference-seqs-IGHV-2015-11-05.fa" "$outdir/baseline_ca.pdf" "Sequence.ID" "$outdir/baseline_ca.txt"
+bash $dir/tmp/baseline/wrapper.sh 1 1 1 1 0 0 "25:26:38:55:65:104:-" $outdir/new_IMGT_cg.txz "cg" "$dir/tmp/baseline/IMGT-reference-seqs-IGHV-2015-11-05.fa" "$outdir/baseline_cg.pdf" "Sequence.ID" "$outdir/baseline_cg.txt"
+bash $dir/tmp/baseline/wrapper.sh 1 1 1 1 0 0 "25:26:38:55:65:104:-" $outdir/new_IMGT_cm.txz "cm" "$dir/tmp/baseline/IMGT-reference-seqs-IGHV-2015-11-05.fa" "$outdir/baseline_cm.pdf" "Sequence.ID" "$outdir/baseline_cm.txt"
 
 #optional output for naive
 
@@ -280,11 +320,3 @@
 
 echo "---------------- Done! ----------------"
 
-
-
-
-
-
-
-#rm $outdir/HS12RSS.txt
-#rm $outdir/HS23RSS.txt