Set up directories $ . $TESTDIR/setup.sh Set up the executable: loadPulses. $ EXEC=$TESTDIR/../loadPulses #Test loadPulses: input is a pls.h5 file #Test -byread and -bymetric $ PLS_IN=$DATDIR/ecoli_lp.fofn $ CMP_IN_2=$DATDIR/ecoli_lp_tiny.cmp.h5 $ CMP_STDOUT_2=$STDDIR/ecoli_lp_tiny.cmp.h5 $ CMP_OUT_byread_2=$OUTDIR/ecoli_lp_tiny.byread.cmp.h5 $ CMP_OUT_bymetric_2=$OUTDIR/ecoli_lp_tiny.bymetric.cmp.h5 $ METRICS=StartFrame,PulseWidth,WidthInFrames,pkmid,IPD,Light $ rm -f $CMP_OUT_byread_2 $ cp $CMP_IN_2 $CMP_OUT_byread_2 $ $EXEC $PLS_IN $CMP_OUT_byread_2 -metrics $METRICS -byread [INFO] * [loadPulses] started. (glob) loading 2 alignments for movie 1 loading 2 alignments for movie 2 [INFO] * [loadPulses] ended. (glob) $ h5diff -c $CMP_OUT_byread_2 $CMP_STDOUT_2 dataset: and \d+ differences found (re) dataset: and \d+ differences found (re) [1] $ rm -f $CMP_OUT_bymetric_2 $ cp $CMP_IN_2 $CMP_OUT_bymetric_2 $ $EXEC $PLS_IN $CMP_OUT_bymetric_2 -metrics $METRICS -bymetric [INFO] * [loadPulses] started. (glob) loading 2 alignments for movie 1 loading 2 alignments for movie 2 [INFO] * [loadPulses] ended. (glob) $ h5diff -c $CMP_OUT_bymetric_2 $CMP_STDOUT_2 dataset: and \d+ differences found (re) dataset: and \d+ differences found (re) [1] #Test loadPulses for deep sorted cmp.h5 $ FOFN_IN=$DATDIR/ecoli_lp.fofn $ CMP_IN_SORTED=$DATDIR/ecoli_lp_tiny_sorted.cmp.h5 $ CMP_STDOUT_SORTED=$STDDIR/ecoli_lp_tiny_sorted.cmp.h5 $ CMP_OUT_SORTED_bymetric=$OUTDIR/ecoli_lp_tiny_sorted_bymetric.cmp.h5 $ CMP_OUT_SORTED_byread=$OUTDIR/ecoli_lp_tiny_sorted_byread.cmp.h5 $ METRICS=StartFrame,PulseWidth,WidthInFrames,pkmid,IPD,Light,DeletionQV,InsertionQV,SubstitutionQV,MergeQV,QualityValue,DeletionTag,SubstitutionTag,ClassifierQV,PreBaseFrames,PulseIndex $ rm -f $CMP_OUT_SORTED_bymetric $ cp $CMP_IN_SORTED $CMP_OUT_SORTED_bymetric $ $EXEC $FOFN_IN $CMP_OUT_SORTED_bymetric -bymetric -metrics $METRICS > $OUTDIR/tmp.log [INFO] * [loadPulses] started. (glob) [INFO] * [loadPulses] ended. (glob) $ h5diff -c $CMP_OUT_SORTED_bymetric $CMP_STDOUT_SORTED dataset: and \d+ differences found (re) dataset: and \d+ differences found (re) [1] $ rm -f $CMP_OUT_SORTED_byread $ cp $CMP_IN_SORTED $CMP_OUT_SORTED_byread $ $EXEC $FOFN_IN $CMP_OUT_SORTED_byread -byread -metrics $METRICS > $OUTDIR/tmp.log [INFO] * [loadPulses] started. (glob) [INFO] * [loadPulses] ended. (glob) $ h5diff -c $CMP_OUT_SORTED_bymetric $CMP_STDOUT_SORTED dataset: and \d+ differences found (re) dataset: and \d+ differences found (re) [1] #Test loadPulses for a zero-alignment cmp.h5 file. $ FOFN_IN=$DATDIR/ecoli_lp.fofn $ CMP_IN_NOALN=$DATDIR/noaln_lp.cmp.h5 $ $EXEC $FOFN_IN $CMP_IN_NOALN -byread -metrics $METRICS [INFO] * [loadPulses] started. (glob) WARNING, there is no alignment in the cmp file. [INFO] * [loadPulses] ended. (glob) #Test loadPulses -byMetric with a 'large' bas.h5 file of which the dataset size is greater than maxElements. $ FOFN_IN=$DATDIR/ecoli_lp.fofn $ CMP_IN=$DATDIR/ecoli_lp_tiny_sorted.cmp.h5 $ CMP_OUT=$OUTDIR/ecoli_lp_maxEle.cmp.h5 $ CMP_STDOUT=$STDDIR/ecoli_lp_maxEle.cmp.h5 $ METRICS=QualityValue,MergeQV,InsertionQV,DeletionQV,DeletionTag,PulseWidth,SubstitutionQV,SubstitutionTag $ MAX_ELEMENTS=140000000 $ rm -f $CMP_OUT $ cp $CMP_IN $CMP_OUT $ $EXEC $FOFN_IN $CMP_OUT -bymetric -metrics $METRICS -maxElements $MAX_ELEMENTS [INFO] * [loadPulses] started. (glob) Either the number of elements exceeds maxElement (140000000). Or the estimated memory consumption exceeds maxMemory (4 GB). Loading pulses from .+ by read. (re) loading 2 alignments for movie 1 loading 2 alignments for movie 2 [INFO] * [loadPulses] ended. (glob) $ h5diff -c $CMP_OUT $CMP_STDOUT dataset: and \d+ differences found (re) dataset: and \d+ differences found (re) dataset: and \d+ differences found (re) [1] #Test loadPulses -byMetric on a multi-streaming job. $ FOFN_IN=$DATDIR/lambda_bax.fofn $ CMP_IN=$DATDIR/lambda_bax.cmp.h5 $ CMP_OUT=$OUTDIR/lambda_bax.cmp.h5 $ CMP_STDOUT=$STDDIR/lambda_bax.cmp.h5 $ METRICS=QualityValue,MergeQV,InsertionQV,DeletionQV,DeletionTag,PulseWidth,SubstitutionQV,SubstitutionTag $ rm -f $CMP_OUT $ cp $CMP_IN $CMP_OUT $ $EXEC $FOFN_IN $CMP_OUT -bymetric -metrics $METRICS [INFO] * [loadPulses] started. (glob) WARNING: There is insufficient data to compute metric: MergeQV in the file .+ It will be ignored. (re) loading 2 alignments for movie 1 loading 2 alignments for movie 1 [INFO] * [loadPulses] ended. (glob) $ h5diff -c $CMP_OUT $CMP_STDOUT dataset: and \d+ differences found (re) dataset: and \d+ differences found (re) dataset: and \d+ differences found (re) [1] #Test loadPulses -bymetric for a ccs cmp.h5 file generated from multiple movies. $ FOFN_IN=$DATDIR/ccs_lp.fofn $ CMP_IN=$DATDIR/ccs_lp.cmp.h5 $ CMP_OUT=$OUTDIR/ccs_lp.cmp.h5 # The original pls.h5 files disappeared, to use another dataset instead. $ rm -f CMP_OUT $ cp $CMP_IN $CMP_OUT $ $EXEC $FOFN_IN $CMP_OUT -bymetric -metrics QualityValue [INFO] * [loadPulses] started. (glob) loading 100 alignments for movie 1 loading 45 alignments for movie 2 [INFO] * [loadPulses] ended. (glob) $ h5ls -r $CMP_OUT | grep "AlnInfo" /AlnInfo Group /AlnInfo/AlnIndex Dataset {145/Inf, 22} /AlnInfo/NumPasses Dataset {145/Inf} #Test loadPulses *.fofn cmp.h5 where *.fofn can either contain ccs.h5 or bas.h5 # and the cmp.h5 s readType is CCS $ CCS_FOFN=$DATDIR/test_ccs.fofn $ BAS_FOFN=$DATDIR/test_bas.fofn $ CMP_IN=$DATDIR/test_ccs_bas.cmp.h5 $ CCS_OUT=$OUTDIR/test_ccs_bas_ccs.cmp.h5 $ BAS_OUT=$OUTDIR/test_ccs_bas_bas.cmp.h5 $ cp $CMP_IN $CCS_OUT $ cp $CMP_IN $BAS_OUT $ $EXEC $CCS_FOFN $CCS_OUT -metrics QualityValue,DeletionQV,DeletionTag,InsertionQV,SubstitutionQV [INFO] * [loadPulses] started. (glob) loading 11 alignments for movie 1 [INFO] * [loadPulses] ended. (glob) $ sleep 1 $ $EXEC $BAS_FOFN $BAS_OUT -metrics QualityValue,DeletionQV,DeletionTag,InsertionQV,SubstitutionQV [INFO] * [loadPulses] started. (glob) loading 11 alignments for movie 1 [INFO] * [loadPulses] ended. (glob) $ h5diff $CCS_OUT $BAS_OUT dataset: and (glob) * differences found (glob) dataset: and * differences found (glob) [1]