Merge pull request #6 from colindaven/dev

Make run_test.sh clearer

run_test.sh

@@ -1,15 +1,24 @@
 #!/bin/bash
-# Colin Davenport, April 2021
+# Colin Davenport, Dec 2021
 
-oligo="ATC"
-echo "running command for oligo $oligo"
 cargo build
+oligo="ATC"
 #cargo run -q  && cat test.fastq  | target/debug/rs_demultiplex  --remove --barcode $oligo > $oligo.txt
+
+oligo="ATC"
+echo "INFO: running command for oligo $oligo, note --remove is given. Read and qual should be len($oligo) bp shorter"
 cat test.fastq  | target/debug/rs_demultiplex  --remove --barcode $oligo > $oligo.txt
 
-echo "produced this output - head"
+echo "INFO: produced this output - head -n 12"
+head -n 12 $oligo.txt
+
+oligo="AAT"
+echo "INFO: running command for oligo $oligo, note --remove not given. Reads should be original length."
+cat test.fastq  | target/debug/rs_demultiplex --barcode $oligo > $oligo.txt
+
+echo "INFO: produced this output - head -n 12"
 head -n 12 $oligo.txt
 
-echo "removing file"
-rm $oligo.txt
+#echo "removing file"
+#rm $oligo.txt