Make sure the test will really pass

   [WARNING] Some reference contigs aligned against are not found in the reference FASTA.  Will process only those contigs supported by the reference FASTA.

--- a/tests/cram/quiver-noqvs-test.t

+++ b/tests/cram/quiver-noqvs-test.t

@@ -9,7 +9,7 @@ Quiver actually makes one error here, wh

@@ -9,7 +9,8 @@ Quiver actually makes one error here, wh

 but this data is from a really ancient instrument-software version, so

 I'm not all that surprised.

-  $ quiver -pC2.NoQVsModel -x0 -q0 $INPUT -r $REFERENCE -o v.gff -o v.vcf -o css.fa -o css.fq

+  $ quiver -pC2.NoQVsModel -x0 -q0 $INPUT -r $REFERENCE -o v.gff -o v.vcf -o css.fa -o css.fq  2>&1 | tee | grep -v -e H5pyDeprecationWarning -e '\[1\]'

+  $ quiver -pC2.NoQVsModel -x0 -q0 $INPUT -r $REFERENCE -o v.gff -o v.vcf -o css.fa -o css.fq  2>&1 | tee | grep -v -e H5pyDeprecationWarning

+  [1]

   $ cat v.gff | tr '\t' ' '

   ##gff-version 3

--- a/tests/cram/plurality-compressed.t

+++ b/tests/cram/plurality-compressed.t

@@ -4,7 +4,7 @@ output files are created correctly.

@@ -4,7 +4,8 @@ output files are created correctly.

   $ export DATA=$TESTDIR/../data

   $ export INPUT=$DATA/hcv/aligned_reads.cmp.h5

   $ export REFERENCE=$DATA/hcv/HCV_Ref_For_187140.fasta

-  $ variantCaller --algorithm=plurality -q 10 -r $REFERENCE -o variants.gff.gz -o consensus.fq.gz $INPUT

+  $ variantCaller --algorithm=plurality -q 10 -r $REFERENCE -o variants.gff.gz -o consensus.fq.gz $INPUT 2>&1 | tee | grep -v -e H5pyDeprecationWarning -e '\[1\]'

+  $ variantCaller --algorithm=plurality -q 10 -r $REFERENCE -o variants.gff.gz -o consensus.fq.gz $INPUT 2>&1 | tee | grep -v -e H5pyDeprecationWarning

+  [1]

 I like to show the head of the output files inline here so that glaringly obvious changes will

 pop right out, but I verify that the files are exactly correct by looking at the md5 sums.