--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/configuration.xml	Mon May 17 15:07:05 2021 +0000
@@ -0,0 +1,293 @@
+<hybridScaffold>
+  <version>
+    <flag attr="version" val0="$Id: hybridScaffold_DLE1_config.xml 7702 2018-06-25 20:53:51Z apang $"/>
+  </version>
+  <global>
+    <flag attr="maxmem" val0="960" display="Maximum memory (GB)" group="Global options" description="Define the maximum amount of RAM in gigabytes to be used by each process."/>
+    <flag attr="maxthreads" val0="54" display="Max threads" group="Global options" description="Define maximum number of threads to be used by each process."/>
+    <flag attr="maxvirtmem" val0="960"/>
+    <flag attr="RAmem" val0="3" val1="1"/>
+  </global>
+  <fasta2cmap>
+    <flag attr="enzyme" val0="BspQI" display="Enzyme" group="FASTA to CMAP digestion" description="Define single enzyme for in-silico FASTA to CMAP digestion. Avalible enzymes: BspQI, BbvCI, BsmI, BsrDI, BssSI, DLE1."/>
+    <flag attr="channelNum" val0="1" display="Channel number" group="FASTA to CMAP digestion" description="Specify the channel the enzyme was used."/>
+    <flag attr="minLabels" val0="0" display="Minimum label sites" group="FASTA to CMAP digestion" description="Specify minimum number of label sites per digested contig."/>
+    <flag attr="minLength" val0="0" display="Minimum length (Kb)" group="FASTA to CMAP digestion" description="Specify minimum length in Kb of each digested contig."/>
+  </fasta2cmap>
+  <align0>
+    <flag attr="M" val0="1" val1="3"/>
+    <flag attr="ScaleDelta" val0="0.02" val1="15"/>
+    <flag attr="ScaleDeltaBPP"/>
+    <flag attr="hashScaleDelta" val0="2"/>
+    <flag attr="res" val0="2.9"/>
+    <flag attr="FP" val0="0.6"/>
+    <flag attr="FN" val0="0.06"/>
+    <flag attr="sf" val0="0.20"/>
+    <flag attr="sd" val0="0.0"/>
+    <flag attr="sr" val0="0.01"/>
+    <flag attr="extend" val0="1"/>
+    <flag attr="outlier" val0="0.0001"/>
+    <flag attr="endoutlier" val0="0.001"/>
+    <flag attr="PVendoutlier"/>
+    <flag attr="deltaX" val0="12"/>
+    <flag attr="deltaY" val0="12"/>
+    <flag attr="xmapchim" val0="12"/>
+    <flag attr="hashgen" val0="5" val1="7" val2="2.4" val3="1.5" val4="0.05" val5="5.0" val6="1" val7="1" val8="4"/>
+    <flag attr="hash" val0="-hashdelta" val1="26" val2="10" val3="46"/>
+    <flag attr="hashMultiMatch" val0="30" val1="10"/>
+    <flag attr="insertThreads" val0="54"/>
+    <flag attr="nosplit" val0="2"/>
+    <flag attr="biaswt" val0="0"/>
+    <flag attr="T" val0="1e-10" display="P-value" group="Initial alignment" description="Minimum confidence value to output initial alignments. Recommended starting value of 1e-5/genome size in Mb."/>
+    <flag attr="S" val0="-1000"/>
+    <flag attr="indel"/>
+    <flag attr="PVres" val0="2"/>
+    <flag attr="rres" val0="0.9"/>
+    <flag attr="MaxSE" val0="0.5"/>
+    <flag attr="HSDrange" val0="1.0"/>
+    <flag attr="outlierBC"/>
+    <flag attr="xmapUnique" val0="12"/>
+    <flag attr="AlignRes" val0="2."/>
+    <flag attr="outlierExtend" val0="12" val1="24"/>
+    <flag attr="Kmax" val0="12"/>
+    <flag attr="resEstimate"/>
+    <flag attr="f"/>
+    <flag attr="mres" val0="0.9"/>
+  </align0>
+  <align1>
+    <flag attr="res" val0="2.9"/>
+    <flag attr="FP" val0="0.6"/>
+    <flag attr="FN" val0="0.06"/>
+    <flag attr="sf" val0="0.20"/>
+    <flag attr="sd" val0="0.0"/>
+    <flag attr="sr" val0="0.01"/>
+    <flag attr="extend" val0="1"/>
+    <flag attr="outlier" val0="0.0001"/>
+    <flag attr="endoutlier" val0="0.001"/>
+    <flag attr="PVendoutlier"/>
+    <flag attr="deltaX" val0="12"/>
+    <flag attr="deltaY" val0="12"/>
+    <flag attr="xmapchim" val0="12"/>
+    <flag attr="hashgen" val0="5" val1="7" val2="2.4" val3="1.5" val4="0.05" val5="5.0" val6="1" val7="1" val8="4"/>
+    <flag attr="hash" val0="-hashdelta" val1="26" val2="10" val3="46"/>
+    <flag attr="hashMultiMatch" val0="30" val1="10"/>
+    <flag attr="insertThreads" val0="54"/>
+    <flag attr="nosplit" val0="2"/>
+    <flag attr="biaswt" val0="0"/>
+    <flag attr="T" val0="1e-10" display="P-value" group="Initial alignment" description="Minimum confidence value to output initial alignments. Recommended starting value of 1e-5/genome size in Mb."/>
+    <flag attr="S" val0="-1000"/>
+    <flag attr="indel"/>
+    <flag attr="PVres" val0="2"/>
+    <flag attr="rres" val0="0.9"/>
+    <flag attr="MaxSE" val0="0.5"/>
+    <flag attr="HSDrange" val0="1.0"/>
+    <flag attr="outlierBC"/>
+    <flag attr="xmapUnique" val0="12"/>
+    <flag attr="AlignRes" val0="2."/>
+    <flag attr="outlierExtend" val0="12" val1="24"/>
+    <flag attr="Kmax" val0="12"/>
+    <flag attr="resEstimate"/>
+    <flag attr="f"/>
+    <flag attr="mres" val0="0.9"/>
+  </align1>
+  <assignAlignType>
+    <flag attr="T_cutoff" val0="1e-11" display="P-value" group="Chimeric/conflicting alignment flagging" description="Minimum confidence value used to flag chimeric/conflicting alignments. Recommand to set it to be the same as the merge_Tvalue below."/>
+    <flag attr="max_overhang" val0="5" display=""/>
+  </assignAlignType>
+  <cut_conflicts>
+    <flag attr="window_size" val0="10000" display="Distance (bp)" group="Conflict-cut" description="The distance (bp) from a conflicting site within which the chimeric quality score of BioNano genome map labels will be examined"/>
+    <flag attr="min_quality_score_threshold" val0="35" display="Percent (%)" group="Conflict-cut" description="The minimal percentage of molecules spanning to the left and right of a label of interest, thus supporting the BioNano assembly at that region"/>
+    <flag attr="min_coverage_threshold" val0="10" display="Coverage (X)" group="Conflict-cut" description="The minimal number of molecules aligning to a label of interest in the BioNano assembly"/>
+  </cut_conflicts>
+  <mergeNGS_BN>
+    <flag attr="merge_Tvalue" val0="1e-11" display="P-value" group="Merging" description="Minimum confidence value used to merge alignments. Recommand to set it to be the same as the assignAlignType T_cutoff above"/>
+    <flag attr="id_shift" val0="100000" display="BioNano cmap id shift" group="Merging" description="Value to shift the BioNano cmap id to distinguish the BioNano cmaps from sequence cmaps. Recommand to set it to be greater than the number of sequence entries."/>
+    <flag attr="max_merge_rounds" val0="40" display=""/>
+    <flag attr="endoutlier" val0="1e-4" display=""/>
+    <flag attr="outlier" val0="1e-4" display=""/>
+    <flag attr="biaswt" val0="0" display=""/>
+    <flag attr="sd" val0="0.1" display=""/>
+    <flag attr="res" val0="2.9" display=""/>
+    <flag attr="mres" val0="2.9" display=""/>
+    <flag attr="sf" val0="0.2" display=""/>
+    <flag attr="RepeatMask" val0="4" val1="0.01" display=""/>
+    <flag attr="RepeatRec" val0="0.7" val1="0.6" val2="1.4" display=""/>
+    <flag attr="pairmerge" val0="80" val1="0.2" display="Min alignment length and Max endoutlier" group="Merging" description="Minimum alignment length required for pair merge, and the maximum endoutlier allowed."/>
+    <flag attr="maxmem" val0="960" display=""/>
+    <flag attr="pairmergeRepeat"/>
+    <flag attr="NoBpp"/>
+    <flag attr="first" val0="-1" display=""/>
+    <flag attr="f"/>
+  </mergeNGS_BN>
+  <align_final_1st_pass>
+    <flag attr="res" val0="2.9"/>
+    <flag attr="FP" val0="0.6"/>
+    <flag attr="FN" val0="0.06"/>
+    <flag attr="sf" val0="0.20"/>
+    <flag attr="sd" val0="0.0"/>
+    <flag attr="sr" val0="0.01"/>
+    <flag attr="extend" val0="1"/>
+    <flag attr="outlier" val0="0.0001"/>
+    <flag attr="endoutlier" val0="0.001"/>
+    <flag attr="PVendoutlier"/>
+    <flag attr="deltaX" val0="12"/>
+    <flag attr="deltaY" val0="12"/>
+    <flag attr="xmapchim" val0="12"/>
+    <flag attr="hashgen" val0="5" val1="7" val2="2.4" val3="1.5" val4="0.05" val5="5.0" val6="1" val7="1" val8="4"/>
+    <flag attr="hash" val0="-hashdelta" val1="26" val2="10" val3="46"/>
+    <flag attr="hashMultiMatch" val0="30" val1="10"/>
+    <flag attr="insertThreads" val0="54"/>
+    <flag attr="nosplit" val0="2"/>
+    <flag attr="biaswt" val0="0"/>
+    <flag attr="T" val0="1e-10" display="P-value" group="Initial alignment" description="Minimum confidence value to output intial alignments. Recommended starting value of 1e-5/genome size in Mb."/>
+    <flag attr="S" val0="-1000"/>
+    <flag attr="indel"/>
+    <flag attr="PVres" val0="2"/>
+    <flag attr="rres" val0="0.9"/>
+    <flag attr="MaxSE" val0="0.5"/>
+    <flag attr="HSDrange" val0="1.0"/>
+    <flag attr="outlierBC"/>
+    <flag attr="xmapUnique" val0="12"/>
+    <flag attr="AlignRes" val0="2."/>
+    <flag attr="outlierExtend" val0="6" val1="24"/>
+    <flag attr="Kmax" val0="6"/>
+    <flag attr="resEstimate"/>
+    <flag attr="f"/>
+    <flag attr="mres" val0="0.9"/>
+    <flag attr="MultiMatches" val0="5"/>
+  </align_final_1st_pass>
+  <align_final_2nd_pass>
+    <flag attr="res" val0="2.9"/>
+    <flag attr="FP" val0="0.6"/>
+    <flag attr="FN" val0="0.06"/>
+    <flag attr="sf" val0="0.20"/>
+    <flag attr="sd" val0="0.0"/>
+    <flag attr="sr" val0="0.01"/>
+    <flag attr="extend" val0="1"/>
+    <flag attr="outlier" val0="0.0001"/>
+    <flag attr="endoutlier" val0="0.001"/>
+    <flag attr="PVendoutlier"/>
+    <flag attr="deltaX" val0="12"/>
+    <flag attr="deltaY" val0="12"/>
+    <flag attr="xmapchim" val0="12"/>
+    <flag attr="hashgen" val0="5" val1="3" val2="2.4" val3="1.5" val4="0.05" val5="5.0" val6="1" val7="1" val8="4"/>
+    <flag attr="hash" val0="-hashdelta" val1="50"/>
+    <flag attr="hashMultiMatch" val0="30" val1="10" val2="3"/>
+    <flag attr="insertThreads" val0="54"/>
+    <flag attr="nosplit" val0="2"/>
+    <flag attr="biaswt" val0="0"/>
+    <flag attr="T" val0="1e-10" display="P-value" group="Final alignment" description="Minimum confidence score used to align NGS contigs back to hybrid scaffold."/>
+    <flag attr="S" val0="-1000"/>
+    <flag attr="indel"/>
+    <flag attr="PVres" val0="2"/>
+    <flag attr="rres" val0="0.9"/>
+    <flag attr="MaxSE" val0="0.5"/>
+    <flag attr="HSDrange" val0="1.0"/>
+    <flag attr="outlierBC"/>
+    <flag attr="xmapUnique" val0="12"/>
+    <flag attr="AlignRes" val0="2."/>
+    <flag attr="outlierExtend" val0="12" val1="24"/>
+    <flag attr="Kmax" val0="12"/>
+    <flag attr="resEstimate"/>
+    <flag attr="f"/>
+    <flag attr="mres" val0="0.9"/>
+    <flag attr="MultiMatches" val0="5"/>
+  </align_final_2nd_pass>
+  <align_final_BNG>
+    <flag attr="res" val0="2.9"/>
+    <flag attr="FP" val0="0.6"/>
+    <flag attr="FN" val0="0.06"/>
+    <flag attr="sf" val0="0.20"/>
+    <flag attr="sd" val0="0.0"/>
+    <flag attr="sr" val0="0.01"/>
+    <flag attr="extend" val0="1"/>
+    <flag attr="outlier" val0="0.0001"/>
+    <flag attr="endoutlier" val0="0.001"/>
+    <flag attr="PVendoutlier"/>
+    <flag attr="deltaX" val0="6"/>
+    <flag attr="deltaY" val0="6"/>
+    <flag attr="xmapchim" val0="12"/>
+    <flag attr="hashgen" val0="5" val1="7" val2="2.4" val3="1.5" val4="0.05" val5="5.0" val6="1" val7="1" val8="4"/>
+    <flag attr="hash" val0="-hashdelta" val1="26" val2="10" val3="46"/>
+    <flag attr="hashMultiMatch" val0="30" val1="10"/>
+    <flag attr="insertThreads" val0="4"/>
+    <flag attr="nosplit" val0="2"/>
+    <flag attr="biaswt" val0="0"/>
+    <flag attr="T" val0="1e-10" display="P-value" group="Final alignment" description="Minimum confidence score used to align NGS contigs back to hybrid scaffold."/>
+    <flag attr="S" val0="-1000"/>
+    <flag attr="indel"/>
+    <flag attr="PVres" val0="2"/>
+    <flag attr="rres" val0="0.9"/>
+    <flag attr="MaxSE" val0="0.5"/>
+    <flag attr="HSDrange" val0="1.0"/>
+    <flag attr="outlierBC"/>
+    <flag attr="xmapUnique" val0="14"/>
+    <flag attr="AlignRes" val0="2."/>
+    <flag attr="outlierExtend" val0="6" val1="24"/>
+    <flag attr="Kmax" val0="6"/>
+    <flag attr="resEstimate"/>
+    <flag attr="BestRef" val0="1"/>
+    <flag attr="f"/>
+    <flag attr="mres" val0="0.9"/>
+  </align_final_BNG>
+  <refineFinal1>
+    <flag attr="refine" val0="1" display="Refine Map" group="Final Refinement" default0="3"/>
+    <flag attr="usecolor" val0="1" default0="1" display="Color Channel" group="Final Refinement"/>
+    <flag attr="A" val0="5" display="Aligned Sites Threshold" group="Final Refinement" default0="5"/>
+    <flat attr="S" val0="-9"/>
+    <flag attr="L" val0="130"/>
+    <flag attr="maptype" val0="0"/>
+    <flag attr="extend" val0="1" display="Allow Extended Molecule" group="Final Refinement" default0="1"/>
+    <flag attr="MaxCov" val0="100" display="Max Coverage" group="Final Refinement" default0="100"/>
+    <flag attr="Mprobeval" display="Fast Mode" group="Final Refinement"/>
+    <flag attr="splitcnt"/>
+    <flag attr="splitrev" val0="2"/>
+    <flag attr="CmapSNR"/>
+    <flag attr="splitsite"/>
+    <flag attr="MinSplitLen" val0="50.0"/>
+    <flag attr="MaxSE" val0="0.5"/>
+    <flag attr="outlier" val0="2e-2" display="Min Outliers P-value" group="Second Refinement" default0="1e-5"/>
+    <flag attr="outlierMax" val0="80."/>
+    <flag attr="outlierLambda" val0="20."/>
+    <flag attr="endoutlier" val0="1e-3" display="Molecule Ends P-value Cutoff" group="Second Refinement" default0="1e-4"/>
+    <flag attr="endoutlierRef" val0="1e-4" val1="1e-3"/>
+    <flag attr="skip_dist" val0="0.0" val2="0.0"/>
+    <flag attr="endoutlierFinal" val0="1"/>
+    <flag attr="maxEnd" val0="90."/>
+    <flag attr="RTHETA_FIX" val0="0"/>
+    <flag attr="TB" val0="1e-6" val1="1e-6" val2="-TBmult" val3="0.1"/>
+    <flag attr="nosplit" val0="2" display="Allow Chimeric Split" group="Final Refinement" default0="2"/>
+    <flag attr="EndTrim" val0="0.0" display="Min End Trim Coverage" group="Final Refinement" default0="4.99"/>
+    <flag attr="biaswt" val0="0.7" display="Bias" group="Final Refinement" default0="0"/>
+    <flag attr="biaswtEnd" val0="0.0"/>
+    <flag attr="biaswtRefine" val0="0.7" val2="1"/>
+    <flag attr="biaswtOutlier" val0="0.0"/>
+    <flag attr="LRbias" val0="1e0" display="Soft Threshold" group="Final Refinement" default0="1e2"/>
+    <flag attr="deltaX" val0="6" display="Molecule Labels Metric" group="Final Refinement" default0="4"/>
+    <flag attr="deltaY" val0="7" display="Mapped Labels Metric" group="Final Refinement" default0="6"/>
+    <flag attr="RepeatMask" val0="5" val1="0.01" display="Repeat Mask P-values" group="Final Refinement" default0="2" default1="0.01"/>
+    <flag attr="RepeatRec" val0="0.7" val1="0.6" val2="1.4"/>
+    <flag attr="CovTrim" val0="2"/>
+    <flag attr="CovTrimLen" val0="55"/>
+    <flag attr="TrimNorm" val0="0"/>
+    <flag attr="TrimNormMed" val0="100"/>
+    <flag attr="TrimNormChim" val0="2"/>
+    <flag attr="TrimNormMin" val0="2"/>
+    <flag attr="PVres" val0="2"/>
+    <flag attr="PVendoutlier"/>
+    <flag attr="AlignRes" val0="1.5"/>
+    <flag attr="rres" val0="1.2"/>
+    <flag attr="cres" val0="5.6" val1="3" val2="0.1"/>
+    <flag attr="hashgen" val00="5" val01="3" val02="2.4" val03="1.5" val04="0.05" val05="5.0" val06="1" val07="1" val08="3"/>
+    <flag attr="hash" val00="-hashdelta" val01="10" val02="10" val03="-mres" val04="0.9"/>
+    <flag attr="HSDrange" val0="1.0"/>
+    <flag attr="hashoffset" val0="1"/>
+    <flag attr="hashMultiMatch" val0="15"/>
+    <flag attr="insertThreads" val0="54"/>
+    <flag attr="BestRef" val0="1"/>
+    <flag attr="BestRefPV" val0="1"/>
+    <flag attr="ChimQuality"/>
+    <flag attr="f" display="Overwrite Output Files" group="Final Refinement"/>
+    <flag attr="T" val0="1e-11" display="P Value Cutoff Threshold"/>
+  </refineFinal1>
+</hybridScaffold>