diff --git a/.classpath b/.classpath
index 58dfa51d..0ee273a9 100644
--- a/.classpath
+++ b/.classpath
@@ -8,7 +8,6 @@
 	<classpathentry kind="lib" path="LibraryJars/bytecode.jar"/>
 	<classpathentry kind="lib" path="LibraryJars/bzip2.jar"/>
 	<classpathentry kind="lib" path="LibraryJars/commons-beanutils.jar"/>
-	<classpathentry kind="lib" path="LibraryJars/commons-codec-1.3.jar"/>
 	<classpathentry kind="lib" path="LibraryJars/commons-collections-3.0.jar"/>
 	<classpathentry kind="lib" path="LibraryJars/commons-collections-3.1.jar"/>
 	<classpathentry kind="lib" path="LibraryJars/commons-collections-testframework-3.0.jar"/>
@@ -69,5 +68,6 @@
 	<classpathentry kind="lib" path="LibraryJars/minimal-json-0.9.4.jar"/>
 	<classpathentry kind="lib" path="LibraryJars/mongo-java-driver-2.14.2.jar"/>
 	<classpathentry kind="lib" path="LibraryJars/json-20140107.jar"/>
+	<classpathentry kind="lib" path="LibraryJars/commons-codec-1.10.jar"/>
 	<classpathentry kind="output" path="Classes"/>
 </classpath>
diff --git a/Documentation/USeqDocumentation/cmdLnMenus.html b/Documentation/USeqDocumentation/cmdLnMenus.html
index d4d074fc..1535610e 100644
--- a/Documentation/USeqDocumentation/cmdLnMenus.html
+++ b/Documentation/USeqDocumentation/cmdLnMenus.html
@@ -1,5 +1,5 @@
 
-			<html><head><title>USeq Command Line Menus 9.0.5
+			<html><head><title>USeq Command Line Menus 9.0.8
 			</title><style type=text/css>#rt{text-align:right; color: #000000; font-weight: bold}
 			#grBk {background-color: #CC9966;}TD {font-family: Verdana, Arial, Helvetica, sans-serif;
 			font-size:12;}H1 {color: #996633; font:arial; font-size:16;}H2 {color: #996633;
@@ -11,18 +11,12 @@
 			<H1>Command Line Menus</H1> <p>
 			
 		
-					<a href="#ABITraceTCPeakCalculator">ABITraceTCPeakCalculator</a><br>
-				
-					<a href="#AdetexBafVCFParser">AdetexBafVCFParser</a><br>
-				
 					<a href="#AggregatePlotter">AggregatePlotter</a><br>
 				
 					<a href="#AggregateQCStats">AggregateQCStats</a><br>
 				
 					<a href="#AlignmentEndTrimmer">AlignmentEndTrimmer</a><br>
 				
-					<a href="#Alleler">Alleler</a><br>
-				
 					<a href="#AllelicExpressionComparator">AllelicExpressionComparator</a><br>
 				
 					<a href="#AllelicExpressionDetector">AllelicExpressionDetector</a><br>
@@ -37,14 +31,8 @@ <H1>Command Line Menus</H1> <p>
 				
 					<a href="#BamContextInspector">BamContextInspector</a><br>
 				
-					<a href="#BamIntensityJoiner">BamIntensityJoiner</a><br>
-				
-					<a href="#BamNMerIntensityParser">BamNMerIntensityParser</a><br>
-				
 					<a href="#BamHg19ToB37Converter">BamHg19ToB37Converter</a><br>
 				
-					<a href="#BamSurgeonMutator">BamSurgeonMutator</a><br>
-				
 					<a href="#BamBlaster">BamBlaster</a><br>
 				
 					<a href="#BamMixer">BamMixer</a><br>
@@ -53,8 +41,6 @@ <H1>Command Line Menus</H1> <p>
 				
 					<a href="#Bar2USeq">Bar2USeq</a><br>
 				
-					<a href="#BaseClassifier">BaseClassifier</a><br>
-				
 					<a href="#Bed2Bar">Bed2Bar</a><br>
 				
 					<a href="#BedStats">BedStats</a><br>
@@ -75,8 +61,6 @@ <H1>Command Line Menus</H1> <p>
 				
 					<a href="#ChIPSeq">ChIPSeq</a><br>
 				
-					<a href="#CHPCAligner">CHPCAligner</a><br>
-				
 					<a href="#ClusterMultiSampleVCF">ClusterMultiSampleVCF</a><br>
 				
 					<a href="#CollectBamStats">CollectBamStats</a><br>
@@ -97,12 +81,6 @@ <H1>Command Line Menus</H1> <p>
 				
 					<a href="#CorrelationMaps">CorrelationMaps</a><br>
 				
-					<a href="#ConvertFastaA2G">ConvertFastaA2G</a><br>
-				
-					<a href="#ConvertFastqA2G">ConvertFastqA2G</a><br>
-				
-					<a href="#ConvertFasta2GCBoolean">ConvertFasta2GCBoolean</a><br>
-				
 					<a href="#ConvertFasta2GCBarGraph">ConvertFasta2GCBarGraph</a><br>
 				
 					<a href="#DefinedRegionBisSeq">DefinedRegionBisSeq</a><br>
@@ -117,11 +95,7 @@ <H1>Command Line Menus</H1> <p>
 				
 					<a href="#EnrichedRegionMaker">EnrichedRegionMaker</a><br>
 				
-					<a href="#ElandMultiParser">ElandMultiParser</a><br>
-				
-					<a href="#ElandParser">ElandParser</a><br>
-				
-					<a href="#ElandSequenceParser">ElandSequenceParser</a><br>
+					<a href="#EstimateErrorRates">EstimateErrorRates</a><br>
 				
 					<a href="#ExportExons">ExportExons</a><br>
 				
@@ -151,8 +125,6 @@ <H1>Command Line Menus</H1> <p>
 				
 					<a href="#FileSplitter">FileSplitter</a><br>
 				
-					<a href="#FilterDuplicateAlignments">FilterDuplicateAlignments</a><br>
-				
 					<a href="#FoundationVcfComparator">FoundationVcfComparator</a><br>
 				
 					<a href="#FoundationXml2Vcf">FoundationXml2Vcf</a><br>
@@ -185,8 +157,6 @@ <H1>Command Line Menus</H1> <p>
 				
 					<a href="#MafParser">MafParser</a><br>
 				
-					<a href="#MaqSnps2Bed">MaqSnps2Bed</a><br>
-				
 					<a href="#MakeSpliceJunctionFasta">MakeSpliceJunctionFasta</a><br>
 				
 					<a href="#MakeTranscriptome">MakeTranscriptome</a><br>
@@ -229,7 +199,7 @@ <H1>Command Line Menus</H1> <p>
 				
 					<a href="#MultiSampleVCFFilter">MultiSampleVCFFilter</a><br>
 				
-					<a href="#MuTectVCFParser">MuTectVCFParser</a><br>
+					<a href="#MutectVCFParser">MutectVCFParser</a><br>
 				
 					<a href="#NovoalignBisulfiteParser">NovoalignBisulfiteParser</a><br>
 				
@@ -263,8 +233,6 @@ <H1>Command Line Menus</H1> <p>
 				
 					<a href="#QueryIndexer">QueryIndexer</a><br>
 				
-					<a href="#Qseq2Fastq">Qseq2Fastq</a><br>
-				
 					<a href="#RandomizeTextFile">RandomizeTextFile</a><br>
 				
 					<a href="#RankedSetAnalysis">RankedSetAnalysis</a><br>
@@ -297,8 +265,6 @@ <H1>Command Line Menus</H1> <p>
 				
 					<a href="#SamTranscriptomeParser">SamTranscriptomeParser</a><br>
 				
-					<a href="#SamFixer">SamFixer</a><br>
-				
 					<a href="#SamSplitter">SamSplitter</a><br>
 				
 					<a href="#SamReadDepthSubSampler">SamReadDepthSubSampler</a><br>
@@ -311,10 +277,6 @@ <H1>Command Line Menus</H1> <p>
 				
 					<a href="#ScanSeqs">ScanSeqs</a><br>
 				
-					<a href="#ShiftAnnotationPositions">ShiftAnnotationPositions</a><br>
-				
-					<a href="#SoapV1Parser">SoapV1Parser</a><br>
-				
 					<a href="#SubtractRegions">SubtractRegions</a><br>
 				
 					<a href="#ScoreChromosomes">ScoreChromosomes</a><br>
@@ -341,8 +303,6 @@ <H1>Command Line Menus</H1> <p>
 				
 					<a href="#Telescriptor">Telescriptor</a><br>
 				
-					<a href="#TQuery">TQuery</a><br>
-				
 					<a href="#UCSCBig2USeq">UCSCBig2USeq</a><br>
 				
 					<a href="#USeq2UCSCBig">USeq2UCSCBig</a><br>
@@ -351,12 +311,16 @@ <H1>Command Line Menus</H1> <p>
 				
 					<a href="#VarScanVCFParser">VarScanVCFParser</a><br>
 				
+					<a href="#VCFBackgroundScanner">VCFBackgroundScanner</a><br>
+				
 					<a href="#VCF2Bed">VCF2Bed</a><br>
 				
 					<a href="#VCFAnnotator">VCFAnnotator</a><br>
 				
 					<a href="#VCFComparator">VCFComparator</a><br>
 				
+					<a href="#VCFConsensus">VCFConsensus</a><br>
+				
 					<a href="#VCFMerger">VCFMerger</a><br>
 				
 					<a href="#VCFVariantMaker">VCFVariantMaker</a><br>
@@ -387,40 +351,6 @@ <H1>Command Line Menus</H1> <p>
 				
 			<br><p>
 		
-					<a name="ABITraceTCPeakCalculator"><pre>**************************************************************************************
-**                        ABI Trace TC Peak Calculator: July 2009                   **
-**************************************************************************************
-Uses a sliding window to estimate the mean T peak area, compares it to the observed
-T area for a given T or C to estimate the fraction T.  Useful for calculating the 
-fraction of converted Cs from bisufite treated DNA in a methylation experiment.
-
-Required Parameters:
--f Full path file text for tab delimited text ABI trace file.
--w Window size in bp for estimating mean T peak areas, defaults to 16.
--c Print only T and C bases, defaults to all.
-
-Example: java -jar pathTo/Apps/ABITraceTCPeakCalculator -f /MyBisSeqData/exp1.txt -c
-
-**************************************************************************************
-</pre><br><p>
-				
-					<a name="AdetexBafVCFParser"><pre>**************************************************************************************
-**                              ADTex VCFParser: Jan 2015                           **
-**************************************************************************************
-Parses VCF files containing Tumor and Normal samples to generate a ADTex B allele
-frequency table.  VarScan2 outputs all variants in T or N regardless of somatic state.
-
-Required Options:
--v Full path file or directory containing xxx.vcf(.gz/.zip OK) file(s).
--m Minimum read coverage, defaults to 20
--n Normal sample index, defaults to 0
--t Tumor sample index, defaults to 1
-
-Example: java -jar pathToUSeq/Apps/VarScanVCFParser -v /VarScan2/VCFFiles/
-
-**************************************************************************************
-</pre><br><p>
-				
 					<a name="AggregatePlotter"><pre>**************************************************************************************
 **                            Aggregate Plotter:  August 2012                       **
 **************************************************************************************
@@ -516,31 +446,6 @@ <H1>Command Line Menus</H1> <p>
 3) java -Xmx4G -jar /path/to/AlignmentEndTrimmer -i 1000X1.test.bam 
            -o 100X1.test.trim.bam -r /path/to/hg19.fasta -v
 **************************************************************************************
-</pre><br><p>
-				
-					<a name="Alleler"><pre>**************************************************************************************
-**                                Alleler:  Sept 2010                               **
-**************************************************************************************
-Intersects a list of alleles (SNPs and INDELs) with gene models and returns their
-affects on coding sequences and splice-junctions. Assumes interbase coordinates. If
-ambiguious bases (ie R,Y,S,W,K,M) are provided the non-reference base is assumed.
-
-Options:
--a Full path file text for a table of alleles.
--e Print an example of an allele table.
--u UCSC RefFlat or RefSeq gene table file, full path. See,
-       http://genome.ucsc.edu/cgi-bin/hgTables
--g Full path directory text containing fasta files for reference base calling
-      (e.g. chr1.fasta, chr5.fasta, ...).
--n Neighborhood to include in intergenic intersection, defaults to 1000
--d Print only non-synonymous and splice affector alleles, defaults to all.
--b Print results in bed format, defaults to detailed report.
--c Collapse multiple hits to the same gene producing the same variant.
-
-Example: java -Xmx1500M -jar pathTo/USeq/Apps/Alleler -a /APCSeq/apcFam7Alleles.txt
-      -u /Anno/ucscKnownGenes.txt -g /Anno/Hg18Fastas/ -n 5000 -d -b
-
-**************************************************************************************
 </pre><br><p>
 				
 					<a name="AllelicExpressionComparator"><pre>**************************************************************************************
@@ -741,50 +646,6 @@ <H1>Command Line Menus</H1> <p>
 Example: java -Xmx4G -jar pathTo/USeq/Apps/BamContextInspector -b Bam/rPENormal.bam
 -r rPENormal_calls.bed -r Ref/human_g1k_v37_decoy.fasta -q 20 -m 20 -a 2 
 
-**************************************************************************************
-</pre><br><p>
-				
-					<a name="BamIntensityJoiner"><pre>**************************************************************************************
-**                          Bam Intensity Joiner : July 2013                        **
-**************************************************************************************
-Extracts base level intensity information from the output of modified Picard
-IlluminaBaseCallsToSam app and inserts this into an alignment file. Be sure to 
-syncronize the alignment output (e.g. -oSync in novoalign) so it is in the same order
-as the intensity data.
-
-Options:
--a Full path to sam/bam alignment file with header.
--i Full path to bam intensity file from running the modified IlluminaBasecallsToSam.
--r Full path bam file for saving the merged results.
--q Minimum mapping quality score. Defaults to 20, bigger numbers are more stringent.
-      This is a phred-scaled posterior probability that the mapping position of read
-      is incorrect. For RNA-Seq data from the SamTranscriptomeParser, set this to 0.
--s Maximum alignment score. Defaults to 240, smaller numbers are more stringent.
--m Filter for particular MD fields.
--u Sub sample data, printing only every XXX alignment.
-
-Example: java -Xmx1500M -jar pathTo/USeq/Apps/BamIntensityJoiner -u 10000 -m 101 -a
-      /Alignments/8341X.sam.gz -i /Ints/8341X.bam -r /Merged/8341.bam
-
-**************************************************************************************
-</pre><br><p>
-				
-					<a name="BamNMerIntensityParser"><pre>**************************************************************************************
-**                           Bam NMer Intensity Parser : April 2012                 **
-**************************************************************************************
-Parses a BAM file from a modified Picard IlluminaBaseCallsToSam run on raw Illumina
-sequencing data to extract information regarding N mers.
-
-Options:
--f Full path to a bam file or directory containing such. Multiple files are merged.
--r Full path file name to save results, defaults to a derivative of -f
--n Length of the N mer, defaults to 5.
--q Minimum base quality score, defaults to 20. Only N-mers where all bases pass the
-       threshold are scored.
-
-Example: java -Xmx1500M -jar pathTo/USeq/Apps/BamIntensityParser -f /Data/BamFiles/
-       -n 7 -q 30
-
 **************************************************************************************
 </pre><br><p>
 				
@@ -800,27 +661,6 @@ <H1>Command Line Menus</H1> <p>
 
 Example: java -Xmx1500M -jar pathToUSeq/Apps/BamHg19B37Converter -b . -e ~/b37.bam
 
-**************************************************************************************
-</pre><br><p>
-				
-					<a name="BamSurgeonMutator"><pre>**************************************************************************************
-**                             BamSurgeon Mutator  : June 2015                      **
-**************************************************************************************
-Generates bed files of random SNVs and INDELs for BamSurgeon. Only one variant is made
-per input region.
-
-Required:
--r Full path bed file containing regions in which to create mutations.
--s Number of SNVs to make, set to zero for just INDELS.
-
--i Number of INDELs to make. This plus -s shouldn't exceed the number of regions.
-
-Optional:
--m Max indel size, defaults to 6
--a Allelic ratio, defaults to 0.5. Set to zero for random from 0.1 - 1
-
-Example: java -Xmx10G -jar pathTo/USeq/Apps/RandomMutationGenerator 
-
 **************************************************************************************
 </pre><br><p>
 				
@@ -909,19 +749,6 @@ <H1>Command Line Menus</H1> <p>
       /AnalysisResults/ -i 5000 -h '#6633FF' -g D_rerio_Jul_2010 
       -d 'Final processed chIP-Seq results for Bcd and Hunchback, 30M reads' 
 
-**************************************************************************************
-</pre><br><p>
-				
-					<a name="BaseClassifier"><pre>**************************************************************************************
-**                             Base Classifier : Oct 2012                            **
-**************************************************************************************
-Beta.
-
-Options:
-
-Example: java -Xmx1500M -jar pathTo/USeq/Apps/BamIntensityParser -f /Data/BamFiles/
-       -n 7 -q 30
-
 **************************************************************************************
 </pre><br><p>
 				
@@ -1227,51 +1054,6 @@ <H1>Command Line Menus</H1> <p>
       /Data/PolIIRep1/,/Data/PolIIRep2/ -c /Data/PolIINRep1/,/Data/PolIINRep2/ -s
       /Data/Results/WtVsNull -f /Anno/satelliteRepeats.bed
 
-**************************************************************************************
-</pre><br><p>
-				
-					<a name="CHPCAligner"><pre>**************************************************************************************
-**                                CHPC Aligner: Sept 2013                           **
-**************************************************************************************
-Wrapper for running novoalign on the CHPC clusters. You will need to configure ssh
-keys from CHPC to your data server. See http://linuxproblem.org/art_9.html (might
-need to reset your home dir on alta/moab 'chmod go-w ~/'). Run
-this app at the CHPC.
-
-Required Options:
--i Genome index file on CHPC
--r Working directory on CHPC, this also defines the name of the final data archive
--f First fastq file on the data server
--s (Optional) Second paired end read fastq file on the data server
--a Archive directory on the data server for saving the final alignments
-
-Default Options:
--l Launch jobs, defaults to not launching jobs, inspect and test the shell scripts
-     before committing.
--w Wall time in hours, defaults to 24.
--x Number CPUs, defaults to 16.
--e Administrator email address, defaults to david.nix@hci.utah.edu
--c (Optional) Client email addresses, comma delimited, no spaces.
--b Don't relaunch bad jobs, defaults to making 3 attempts before aborting.
--o CHPC account to draw hours from (e.g. kaplan-em), defaults to kaplan.
--d Raw data user name and server, defaults to u0028003@hci-moab.hci.utah.edu
--g Final alignment data user name and server, defaults to
-     u0028003@hci-moab.hci.utah.edu
--j Aligner application, defaults to 
-     '/uufs/chpc.utah.edu/common/home/hcibcore/tomato/app/novoalign/novoalign'
--p Aligner cmd line options
--n Number of reads to process per job, defaults to 1000000
--k Number of jobs to run, defaults to number of reads per job setting
--t Filter results for lines containing a 'chr' string, defaults to all.
--q Strip @SQ: lines from SAM alignment results, recommended for transcriptomes.
-
-Example: java -Xmx4G -jar pathTo/USeq/Apps/CHPCAlign  -p '-F ILMFQ -t60 -rRandom' 
-    -i ~/Genomes/hg19Splices34bpAdaptersNovo.index
-    -r /scratch/serial/u0028003/7317X1_100602 
-    -f /mnt/hci-ma/MicroarrayData/2010/7317R/GAII/100602_7317X1_s_7_1_sequence.txt.gz 
-    -s /mnt/hci-ma/MicroarrayData/2010/7317R/GAII/100602_7317X1_s_7_2_sequence.txt.gz 
-    -a /mnt/hci-ma/AnalysisData/2010/A115  -w 6 -e nix@gmail.com -t -b 
-
 **************************************************************************************
 </pre><br><p>
 				
@@ -1482,49 +1264,6 @@ <H1>Command Line Menus</H1> <p>
 Example: java -Xmx256M -jar pathTo/T2/Apps/CorrelationMaps -f /Mango/geneFile.txt
        -w 30000 -n 2 -o /Mango/operons.txt
 
-**************************************************************************************
-</pre><br><p>
-				
-					<a name="ConvertFastaA2G"><pre>**************************************************************************************
-**                        Convert Fasta A 2 G: Mar 2012                             **
-**************************************************************************************
-Converts all the a/A's to g/G's in fasta file(s) maintaining case.
-
-Required Parameters:
--f Full path for the fasta file (.fa/.fasta/.gz/.zip OK) or directory containing such.
--s Full path directory to save the converted files.
-
-Example: java -Xmx2G -jar pathTo/Apps/ConvertFastaA2G -f /mm9/Fastas/ -s
-      /mm9/AGConvertedFastas/
-
-**************************************************************************************
-</pre><br><p>
-				
-					<a name="ConvertFastqA2G"><pre>**************************************************************************************
-**                        Convert Fastq A 2 G: Mar 2012                             **
-**************************************************************************************
-Converts all the sequence A's to G's, case insensitive.
-
-Required Parameters:
--f Full path for the fastq file or directory containing such. xxx.gz/.zip OK.
--s Optional, full path directory to save the converted files.
-
-Example: java -Xmx2G -jar pathTo/Apps/ConvertFastqA2G -f /IllData/Fastq/ 
-
-**************************************************************************************
-</pre><br><p>
-				
-					<a name="ConvertFasta2GCBoolean"><pre>**************************************************************************************
-**                       Convert Fasta 2 GC Boolean: Aug 2008                       **
-**************************************************************************************
-Converts fasta file(s) into serialized boolean[]s where every base g or c is true all
-others false. Will also work with xxx.binarySeq files.
-
-Required Parameters:
--f Full path text for the xxx.fasta file or directory containing such.
-
-Example: java -Xmx2000M -jar pathTo/Apps/ConvertFasta2GCBoolean -f /affy/Fastas/
-
 **************************************************************************************
 </pre><br><p>
 				
@@ -1805,71 +1544,38 @@ <H1>Command Line Menus</H1> <p>
 **************************************************************************************
 </pre><br><p>
 				
-					<a name="ElandMultiParser"><pre>**************************************************************************************
-**                          Eland Multi Parser: October 2008                        **
-**************************************************************************************
-Parses an Eland xxx.eland_multi.txt alignment file tabulating hits to each fasta entry.
-Good for scoring hits to a transcriptome where every fasta entry represents a
-different gene.
-
--f The full path directory/file text of your xxx.eland_multi.txt(.zip) file(s). Files
-      will be merged.
--r Full path file text for saving the results.
-
-
-Example: java -Xmx1500M -jar pathToUSeq/Apps/ElandMultipParser -f 
-      /data/MultiFiles/ -r /data/transcriptomeResults.xls 
-
-**************************************************************************************
-</pre><br><p>
-				
-					<a name="ElandParser"><pre>**************************************************************************************
-**                               ElandParser: May 2008                              **
-**************************************************************************************
-Splits and converts Eland Extended xxx_export.txt or xxx_sorted.txt files
-into center position alignment scored binary xxx.bar files. Coordinates are in
-interbase coordiantes (zero based, stop excluded). These can be directly viewed in IGB.
-
--v Versioned Genome (ie hg18, dm2, ce2, mm8), see UCSC Browser,
-      http://genome.ucsc.edu/FAQ/FAQreleases.
--m Minimum aligment score, Phred scale, defaults to 13. Not used with stand alone.
--f The full path directory/file text of your xxx_export.txt(.zip/.gz) or
-      xxx_sorted.txt(.zip/.gz) file(s).
--r Full path directory text for saving the results, defaults to export.txt parent.
--s Shift centered position N bps 3' to accomodate chIP-seq fragment size. Stranded.
-      Note, this is far less than 1/2 the expected fragment size, determine best
-      value by visual inspection of likely positives. Defaults to 0. If you plan on
-      filtering your PointData, don't shift their positions, do it in the filter app.
--p Parse stand alone Eland output file.
-
-Example: java -Xmx1500M -jar pathToUSeq/Apps/ElandParser -f /Solexa/Run7/
-     -v H_sapiens_Mar_2006 -s 38 -r /Solexa/ParsedData/PolIII/
-
-**************************************************************************************
-</pre><br><p>
-				
-					<a name="ElandSequenceParser"><pre>**************************************************************************************
-**                         Eland Sequence Parser: March 2009                        **
+					<a name="EstimateErrorRates"><pre>**************************************************************************************
+**                            Estimate Error Rates: Jan 2017                        **
 **************************************************************************************
-Parses sequence information from Eland Extended alignment summary files. For every
-base, sums the quality scores generating a G, A, T, and C track xxx.bar file for 
-visualization in IGB.  Also generates a consensus track (1-fraction consensus) for
-each base.
-
--f The full path directory/file text of your xxx_export.txt(.zip/.gz) or
-      xxx_sorted.txt(.zip/.gz) file(s).
--r Full path directory text for saving the results.
--g Full path directory text containing fasta files for reference base calling
-      (e.g. chr1.fasta, chr5.fasta).
--v Versioned Genome (ie hg18, dm2, ce2, mm8), see UCSC Browser,
-      http://genome.ucsc.edu/FAQ/FAQreleases.
--a Minimum aligment score, -10Log10(p-value), defaults to 13.
--c Minimum consensus score, -10Log10(p-value), defaults to 60.
+EER scans an mpileup file looking for short windows of adjacent bps (default 7) where
+1) each base exceeds a minimum read depth of high quality bases (>100)
+2) shows little evidence of indels (<0.1), and 
+3) the fraction of poor quality bps isn't excessive (<0.5). 
+The non reference snv observations are then tabulated for the center base in each
+window, if low (<0.1), they are assumed error and saved. For indel error calculations,
+each bp is scored as above sans the indel filter and window requirement. Insertions
+are counted once regardless of the size, where as deletions are counted for every base
+affected. Run this app on samples where real snvs and indels are expected to have an
+allele frequency of  > ~0.5 , e.g. normal or pure single clone somatic.
 
+Required Options:
+-m Path to a normal sample mpileup file (gz/zip OK), 'samtools mpileup -B -q 20 -d 
+     1000000 -f $fastaIndex -l $bedFile *.bam | gzip > mpileup.gz' Multiple samples
+     in the file are merged.
 
-Example: java -Xmx1500M -jar pathToUSeq/Apps/ElandSequenceParser -v hg18 -c 90
-      -f /data/ExportFiles/ -r /data/Results -g /genomes/Hg18Fastas 
+Default Options:
+-b Minimum base quality, default 20
+-r Minimum good base coverage, default 100
+-i Maximum INDEL allele freq for snv counting, default 0.1
+-n Maximum non reference allelic freq, default 0.1
+-p Maximum failing base allele freq, default 0.5
+-f Number flanking bp to define scorable region, default 3
+-s Comma delimited list (zero is 1st sample, no spaces) of sample indexes to merge,
+     defaults to all.
+-c File path to save a count table of parsed observations, defaults to none.
 
+Example: java -Xmx4G -jar pathToUSeq/Apps/EstimateErrorRates -m normExo.mpileup.gz
+     -r 200 -i 0.15 -f 2 -s 0,3,4 -c countTable.txt.gz
 **************************************************************************************
 </pre><br><p>
 				
@@ -1947,7 +1653,7 @@ <H1>Command Line Menus</H1> <p>
 </pre><br><p>
 				
 					<a name="FastqBarcodeTagger"><pre>**************************************************************************************
-**                           Fastq Barcode Tagger: Dec 2015                         **
+**                           Fastq Barcode Tagger: Jan 2017                         **
 **************************************************************************************
 Takes three fastq files (paired end reads and a third containing barcodes), appends
 the barcode and quality to the fastq header, and writes out the modified records. 
@@ -1959,6 +1665,7 @@ <H1>Command Line Menus</H1> <p>
 -i (Optional) Write interlaced fastq to stdout for direct piping to other apps
 -r (Optional) Directory to save the modified fastqs, defaults to the parent of -f
 -l (Optional) Max length of barcode, defaults to all. Use to trim 3' end.
+-a (Optional) Append the line number to the read name to uniquify.
 
 Example: java -Xmx1G -jar pathToUSeq/Apps/FastqBarcodeTagger -f lob_1.fastq.gz
      -s lob_2.fastq.gz -b lob_barcode.fastq.gz -i | bwa mem -p /ref/hg19.fa 
@@ -2129,35 +1836,6 @@ <H1>Command Line Menus</H1> <p>
 
 Example: java -Xmx256M -jar pathTo/T2/FileSplitter -f /affy/bpmap.txt -n 50000
 
-**************************************************************************************
-</pre><br><p>
-				
-					<a name="FilterDuplicateAlignments"><pre>**************************************************************************************
-**                          FilterDuplicateAlignments: Mar 2010                     **
-**************************************************************************************
-Filters alignments for potential amplification bias by randomly selecting X alignments
-from those with the same chromosome, position, and strand. Can also filter for the
-best unique alignment based on read score. Column indexes start with 0.
-
-Options:
--f Full path file/ directory text containing tab delimited alignments.
--r Full path directory for saving the results.
--c Alignment chromosome column index.
--p Alignment position column index, assumes this is always referenced to the + strand
--s Alignment sequence column index.
--t Strand column index.
--m Save a max number of identical alignments, choose number, defaults to random
-        unique sequences.
--b Save only the best alignment per start postion, defined by total score.  Indicate
-        which column contains the quality ascii text.
--j Include splice junction chromosomes in filtering (e.g. chr7_101267544_101272320).
-        Defaults to removing them. (Only keep for RNA-Seq datasets.)
-
-Example: java -Xmx1500M -jar pathToUSeq/Apps/FilterDuplicateAlignments -f
-     /Novoalign/Run7/ -s /Novoalign/Run7/DupFiltered/ -c 7 -p 8 -s 2 -b 3 -t 9
-
-	  Use -c 10 -p 12 -s 8 -t 13 -b 9  for ELAND sorted or export alignments.
-
 **************************************************************************************
 </pre><br><p>
 				
@@ -2511,20 +2189,6 @@ <H1>Command Line Menus</H1> <p>
 Example: java -Xmx4G -jar pathTo/USeq/Apps/MafParser -m MafTCGAFiles/ -o Sorted/ 
               -t ~/BioApps/HTSlib/1.3/bin/ -c 
 
-**************************************************************************************
-</pre><br><p>
-				
-					<a name="MaqSnps2Bed"><pre>**************************************************************************************
-**                              MaqSnps2Bed: June 2009                              **
-**************************************************************************************
-Converts a Maq snp text file (1 based coordinates) into a bed file (interbase 
-      coordinates).  Also writes out an Alleler formated text file.
-
--f Full path file text to the file or directory containing Maq snp txt files.
-
-Example: java -Xmx1000M -jar path2/USeq/Apps/MaqSnps2Bed -f /data/maqSnpFile.txt
-
-
 **************************************************************************************
 </pre><br><p>
 				
@@ -3061,20 +2725,25 @@ <H1>Command Line Menus</H1> <p>
 **************************************************************************************
 </pre><br><p>
 				
-					<a name="MuTectVCFParser"><pre>**************************************************************************************
-**                               MuTect VCF Parser: Nov 2016                        **
+					<a name="MutectVCFParser"><pre>**************************************************************************************
+**                               Mutect VCF Parser: Jan 2017                        **
 **************************************************************************************
-Parses MuTech2 VCF files, filtering for minimum read depth, difference in allelic
-ratios, and allelic fractions. Splits files into pass and fail with no modifications.
+Parses Mutect2 VCF files, filtering for read depth, allele frequency diff ratio, etc.
+Inserts AF and DP into for the tumor sample into the INFO field. Changes the sample
+order to Normal and Tumor and updates the #CHROM line.
 
 Required Options:
 -v Full path file or directory containing xxx.vcf(.gz/.zip OK) file(s).
--a Minimum alignment depth for tumor and normal samples, defaults to 0.
--r Minimum absolute difference in alt allelic ratios, defaults to 0.
--n Maximum normal alt allelic fraction, defaults to 1.
--m Minimum tumor alt allelic fraction, defaults to 0.
+-t Minimum tumor allele frequency (AF), defaults to 0.
+-n Maximum normal AF, defaults to 1.
+-u Minimum tumor alignment depth, defaults to 0.
+-o Minimum normal alignment depth, defaults to 0.
+-d Minimum T-N AF difference, defaults to 0.
+-r Minimum T/N AF ratio, defaults to 0.
+-p Remove non PASS filter field records.
 
-Example: java -jar pathToUSeq/Apps/MuTechVCFParser -v /VCFFiles/ -a 15 -r 0.10
+Example: java -jar pathToUSeq/Apps/MutectVCFParser -v /VCFFiles/ -t 0.05 -n 0.5 -u 100
+        -o 20 -d 0.05 -r 2
 
 **************************************************************************************
 </pre><br><p>
@@ -3509,23 +3178,27 @@ <H1>Command Line Menus</H1> <p>
 </pre><br><p>
 				
 					<a name="QueryIndexer"><pre>**************************************************************************************
-**                                Query Indexer: Nov 2016                           **
+**                                Query Indexer: Feb 2017                           **
 **************************************************************************************
-Builds index files for Query by recursing through a data directory looking for vcf,
-maf, bed, and bedGraph files that have been bgzip compressed and tabix indexed.
-Interval trees are build containing regions that overlap with one or more data sources.
+Builds index files for Query by recursing through a data directory looking for bgzip
+compressed and tabix indexed genomic data files (e.g. vcf, bed, maf, and custom).
+Interval trees are built containing regions that overlap with one or more data sources.
 These are used by the Query REST service to rapidly identify which data files contain
-records that overlap each users query. This app typically needs >20G RAM to run.
+records that overlap user's ROI. This app is threaded for simultanious file loading
+and requires >30G RAM to run on large data collections so use a big analysis server.
+Note, relative file paths are saved. So long as the structure of the Data Directory is
+preserved, the QueryIndexer and Query REST service don't need to run on the same file
+system.
 
 Required Params:
--c A bed file of chromosomes and their lengths (e.g. 21 0 48129895) to use to 
+-c A bed file of chromosomes and their lengths (e.g. chr21 0 48129895) to use to 
      building the intersection index. Exclude those you don't want to index. For
      multiple builds and species, add all, duplicates will be collapsed taking the
      maximum length. Any 'chr' prefixes are ignored when indexing and searching.
--d A data directory containing gzipped tabixed xxx.vcf.gz, xxx.bed.gz, xxx.bedGraph.gz,
-     and xxx.maf.txt.gz files. Recurses through all sub directories. Except for gVCF,
-     Be sure to normalize and decompose_blocksub all VCF records, see 
-     http://genome.sph.umich.edu/wiki/Vt
+-d A data directory containing bgzipped and tabix indexed data files. Known file types
+     include xxx.vcf.gz, xxx.bed.gz, xxx.bedGraph.gz, and xxx.maf.txt.gz. Others will
+     be parsed using info from the xxx.gz.tbi index. Be sure to normalize and
+     decompose_blocksub all VCF records, see http://genome.sph.umich.edu/wiki/Vt
 -t Full path directory containing the compiled bgzip and tabix executables. See
      https://github.com/samtools/htslib
 -i A directory in which to save the index files
@@ -3540,32 +3213,8 @@ <H1>Command Line Menus</H1> <p>
 https://github.com/HuntsmanCancerInstitute/Query
 
 d=/pathToYourLocalGitHubInstalled/Query/TestResources
-java -Xmx50G -jar pathToUSeq/Apps/QueryIndexer -c $d/b37Chr20-21ChromLen.bed -d $d/Data
--i $d/Index -t ~/BioApps/HTSlib/1.3/bin/ -s $d/Data/B37/GVCFs 
-
-**************************************************************************************
-</pre><br><p>
-				
-					<a name="Qseq2Fastq"><pre>**************************************************************************************
-**                                  Qseq2Fastq: Aug 2010                            **
-**************************************************************************************
-Parses, filters out reads failing QC, compresses and converts single and paired read
-qseq files to Illumina fastq format. Does not concatinate tiles.
-
-Required Parameters:
--q Qseq directory. This should contain all of the qseq files for a sequencing run,
-       multiple lanes, paired and single reads. (e.g. s_5_1_0025_qseq.txt(.gz/zip OK))
-
-Optional Parameters:
--f Fastq save directory. Defaults to the qseq directory.
--a Keep all reads. Defaults to removing those failing the QC flag. Paired reads are
-       only removed if both reads fail QC.
--p Print full fastq headers. Defaults to using read count.
--d Delete qseq files upon successfull parsing of all files. Be carefull!
--s Silence non error output.
-
-Example: java -Xmx2G -jar pathTo/USeq/Apps/Qseq2Fastq -f /Runs/7/Fastq -q
-      /Runs/100726_SN141_0265_A207D4ABXX/Data/Intensities/BaseCalls 
+java -Xmx10G -jar pathToUSeq/Apps/QueryIndexer -c $d/b37Chr20-21ChromLen.bed -d $d/Data
+-i $d/Index -t ~/BioApps/HTSlib/1.3/bin/ -s $d/Data/Public/B37/GVCFs 
 
 **************************************************************************************
 </pre><br><p>
@@ -4038,35 +3687,6 @@ <H1>Command Line Menus</H1> <p>
 Example: java -Xmx1500M -jar pathToUSeq/Apps/SamTranscriptomeParser -f /Novo/Run7/
      -m 20 -s /Novo/STPParsedBams/run7.bam -p -r 
 
-**************************************************************************************
-</pre><br><p>
-				
-					<a name="SamFixer"><pre>**************************************************************************************
-**                                 Sam Fixer: August 2011                           **
-**************************************************************************************
-Parses, filters, merges, and fixes xxx.sam files.
-
-Options:
--f The full path file or directory containing xxx.sam(.gz/.zip OK) file(s). Multiple 
-      files will be merged.
--s Full path file name for saving the fixed sam file.
-
-Default Options:
--m Minimum mapping quality score. Defaults to 0, bigger numbers are more stringent.
-      This is a phred-scaled posterior probability that the mapping position of read
-      is incorrect.
--a Maximum alignment score. Defaults to 1000, smaller numbers are more stringent.
--d Don't strip optional MD fields from alignments, defaults to removing these.
--u Remove unmapped reads.
--q Don't remove poor quality reads.
--c Convert splice-junctions to genomic coordinates, by providing a splice junction
-      radius. Only works for single read RNA-Seq data where a splice junction fasta
-      file was included in the alignments from the USeq MakeSpliceJunctionFasta app.
-      This does NOT work for paired RNA-Seq data.
-
-Example: java -Xmx1500M -jar pathToUSeq/Apps/SamParser -f /Novo/Run7/
-     -m 20 -a 120 -s /Novo/Run7/mergedFixed.sam  -c 46 -u
-
 **************************************************************************************
 </pre><br><p>
 				
@@ -4176,23 +3796,24 @@ <H1>Command Line Menus</H1> <p>
 </pre><br><p>
 				
 					<a name="ScalpelVCFParser"><pre>**************************************************************************************
-**                            Scalpel VCF Parser: July 2016                         **
+**                            Scalpel VCF Parser: Jan 2017                         **
 **************************************************************************************
-Filters Scalpel VCF INDEL files for various thresholds.  Replaces the FILTER field 
-with . or FAIL, adds tumor DP and AF values to the info field.
+Filters Scalpel VCF INDEL files for various thresholds.  Adds tumor DP and AF values
+to the info field.
 
 Required Params:
 -v Full path file or directory containing xxx.vcf(.gz/.zip OK) file(s)
 -m Minimum QUAL score, defaults to 0
--a Minimum alignment depth for tumor sample, defaults to 100
--b Minimum alignment depth for normal sample, defaults to 30
--t Minimum tumor alt allelic fraction, defaults to 0.05
--n Maximum normal alt allelic fraction, defaults to 0.1
--r Minimum alt Tum/Norm allelic ratio, defaults to 1.6
--f Mark variants failing thresholds FAIL instead of not printing
+-t Minimum tumor allele frequency (AF), defaults to 0.
+-n Maximum normal AF, defaults to 1.
+-u Minimum tumor alignment depth, defaults to 0.
+-o Minimum normal alignment depth, defaults to 0.
+-d Minimum T-N AF difference, defaults to 0.
+-r Minimum T/N AF ratio, defaults to 0.
+-p Remove non PASS filter field records.
 
-Example: java -jar pathToUSeq/Apps/Scalpel/VCFParser -v /VCFFiles/ -m 150 -a 200
-      -r 2 -n 0.2 -t 0.03  
+Example: java -jar pathToUSeq/Apps/ScalpelVCFParser -v /VCFFiles/ -t 0.05 -n 0.5 -u 100
+        -o 20 -d 0.05 -r 2
 
 **************************************************************************************
 </pre><br><p>
@@ -4244,48 +3865,6 @@ <H1>Command Line Menus</H1> <p>
       /Data/PolIIRep1/,/Data/PolIIRep2/ -c /Data/Input1/,Data/Input2/ -s
       /Data/PolIIResults -w 200 -p 100 -f -g 5 
 
-**************************************************************************************
-</pre><br><p>
-				
-					<a name="ShiftAnnotationPositions"><pre>**************************************************************************************
-**                         Shift Annotation Positions: Oct 2010                     **
-**************************************************************************************
-Uses the information in an xxx.shifter.txt file from the ConcatinateFastas app to
-shift the annotation to match the coordinates of the concatinated sequence. Good for
-working with poorly assembled genomes. Run this multiple times with different shifter
-files. All files are assumed to use interbase coordinates.
-
-Options:
--b Full path file name for a xxx.bed formatted annotation file.
--u (OR) Full path file name for a UCSC refflat/ refseq formatted gene table.
--s Full path file name for the xxx.shifter.txt file from the ConcatinateFastas app.
-
-Example: java -Xmx4G -jar pathTo/USeq/Apps/ShiftAnnotationPositions 
-    -u /zv8/ucscRefSeq.txt -f /zv8/BadFastas/chrScaffold.shifter.txt
-
-**************************************************************************************
-</pre><br><p>
-				
-					<a name="SoapV1Parser"><pre>**************************************************************************************
-**                                SoapV1Parser: Feb 2009                            **
-**************************************************************************************
-Splits and converts Soap version 1 alignment xxx.txt files into center position binary
-PointData xxx.bar files. Interbase coordiantes (zero based, stop excluded).
-These can be directly viewed in IGB.
-
--v Versioned Genome (ie H_sapiens_Mar_2006), see UCSC Browser,
-      http://genome.ucsc.edu/FAQ/FAQreleases.
--f The full path directory/file text of your Soap xxx.txt(.zip or .gz) file(s).
--r Full path directory text for saving the results.
--x Maximum number of best matches, defaults to 1.
--m Miminum read length, defaults to 17.
--s Sum identical PointData positions. This should not be used for any downstream USeq
-      applications, only for visualization.
--p Make read length histogram on reads that pass filters, defaults to all.
-
-Example: java -Xmx1500M -jar pathToUSeq/Apps/SoapV1Parser -f /Soap/Run7/
-     -v H_sapiens_Mar_2006 -x 5 -m 20
-
 **************************************************************************************
 </pre><br><p>
 				
@@ -4569,7 +4148,7 @@ <H1>Command Line Menus</H1> <p>
 </pre><br><p>
 				
 					<a name="TomatoFarmer"><pre>**************************************************************************************
-**                                TomatoFarmer: September 2014                      **
+**                                TomatoFarmer: June 2015                           **
 **************************************************************************************
 TomatoFarmer controls an exome analysis from start to finish.  It creates alignment 
 jobs for each of the samples in your directory, waits for all jobs to finish and then 
@@ -4582,25 +4161,20 @@ <H1>Command Line Menus</H1> <p>
 
 -d Job directory.  This directory must be a subdirectory of /tomato/version/job. Can 
        can be several directory levels below /tomato/version/job. 
-       Example: '-d /tomato/version/job/krustofsky/demo'. 
+       Example: '-d /tomato/dev/job/krustofsky/demo'. 
 -e Email address.  TomatoFarmer emails you once the job completes/fails. You can also
        opt to get all tomato emails as individual jobs start/end (see option -x).
        Example: '-e hershel.krustofsky@hci.utah.edu'.
 -y Analysis pipeline. The analysis pipeline or step to run.  Current options are: 
           Full pipline:
-          1) ugp_full - UGP v1.0.5 pipeline, includes: Alignment, metrics and variant
+          1) ugp_full - UGP v1.3.0 pipeline, includes: Alignment, metrics and variant
              calls. Defaults to bwa and raw variant filtering
-          2) core_full - Core best practices, includes: Alignment, metrics and variant
-             calls.  Defaults to bwa, only raw variant filtering allowed
           Indivdual Steps
-          4) ugp_align - Alignment/recalibration only. Defaults to bwa.
-          5) core_align - Alignment/dedup only. Defalts to bwa.
-          6) metrics - Sample QC metrics only. Requires sample level *raw.bam and 
-             *final.bam files from aligment steps.
+          2) ugp_align - Alignment/recalibration only. Defaults to bwa.
+          6) metrics - Sample QC metrics only. Requires sample level  *final.bam 
+              files from aligment steps.
           7) ugp_variant - Variant detection and filtering. Requires 1 or more 
              *final.bam files from alignment step. Defaults to raw variant filtering.
-          8) core_variant - Variant detection Requires 1 or more *final.bam from 
-             alignment step.
       Example: '-y ugp_full'.
 -p Properties file.  This file contains a list of cluster-specific paths and options 
       this file doesn't need to be changed by the user. Example: '-p properties.txt' 
@@ -4670,35 +4244,6 @@ <H1>Command Line Menus</H1> <p>
 Example: java -Xmx4G -jar pathTo/USeq/Apps/Telescriptor -u hg19EnsTrans.ucsc -t Bam/T
        -c Bam/C -s GV_MOR 
 
-**************************************************************************************
-</pre><br><p>
-				
-					<a name="TQuery"><pre>**************************************************************************************
-**                                    TQuery: Oct 2016                             **
-**************************************************************************************
-TQ returns vcf, maf, and bed records that overlap user's regions in bed or vcf format.
-Strict adherence to bed format is assumed (1st base is 0, last base is not included,
-last base > first; vcf is in 1 base so subtract 1 from pos to convert to bed).
-This app needs > 27G of RAM for human/ mouse/ plant. A two step search is performed
-using an in memory file : bp index to find intersecting regions followed by a tabix
-query to pull the data.  Multiple data source filters can be applied to limit output.
-
-Required Params:
--c A bed file of chromosomes and their lengths (e.g. chr21 0 48129895) to use to 
-     building the intersection index. Note, the chr name must match across all 
-     datasets, no mixing of chr21 and 21.
--d A data directory containing gzipped tabixed (https://github.com/samtools/htslib)
-     vcf, bed, and maf files. Recurses through all sub directories. Be sure to normalize
-     the vcf records with a package like Vt, see http://genome.sph.umich.edu/wiki/Vt .
-     Use the MafParser to sort and tabix your TCGA xxx.maf.txt files.
-
-Default Params:
--n Number of processors to use, defaults to all-1.
--q Number of queries in each lookup chunk, defaults to 1000
-
-Example: java -Xmx64G -jar pathToUSeq/Apps/TQuery -c b37ChrLen.bed 
-     -t TabixDataFiles/ | gzip > results.json.gz  
-
 **************************************************************************************
 </pre><br><p>
 				
@@ -4784,6 +4329,43 @@ <H1>Command Line Menus</H1> <p>
 
 Example: java -jar pathToUSeq/Apps/VarScanVCFParser -v /VarScan2/VCFFiles/
 
+**************************************************************************************
+</pre><br><p>
+				
+					<a name="VCFBackgroundScanner"><pre>**************************************************************************************
+**                           VCF Background Scanner : Jan 2016                      **
+**************************************************************************************
+VBS calculates non-reference allele frequencies (AF) from a background multi-sample 
+mpileup file over each vcf record. It then calculates a z-score for the vcf AF and 
+appends it to the INFO field. If multiple bps are affected (e.g. INDELs) or bp padding
+provided, the lowest bp z-score is appended. Z-scores < ~4 are indicative of non
+reference bps in the background samples. Note, VBS requires an AF tag in the INFO
+field of each record. 
+
+Required:
+-v Path to a xxx.vcf(.gz/.zip OK) file or directory containing such.
+-m Path to a bgzip compressed and tabix indexed multi-sample mpileup file. e.g.:
+      1) Mpileup: 'echo "#SampleOrder: "$(ls *bam) > bkg.mpileup; samtools mpileup
+             -B -q 13 -d 1000000 -f $fastaIndex -l $bedFile *.bam >> bkg.mpileup'
+      2) Bgzip: 'tabix-0.2.6/bgzip bkg.mpileup'
+         Tabix: 'tabix-0.2.6/tabix -s 1 -b 2 -e 2 bkg.mpileup.gz'
+-s Path to directory in which to save the modified vcf file(s)
+
+Optional:
+-i Comma delimited list (zero is 1st sample, no spaces) of mpileup sample indexes to
+     examine, defaults to all.
+-b BP padding, defaults to 0
+-z Minimum vcf z-score, defaults to 0, no filtering
+-q Minimum mpileup sample bp quality, defaults to 20
+-c Minimum mpileup sample read coverge, defaults to 20
+-f Maximum mpileup sample AF, defaults to 0.3
+-a Minimum # mpileup samples for z-score calculation, defaults to 3
+-e Exclude vcf records that could not be z-scored
+-d Print verbose debugging output
+
+Example: java -Xmx4G -jar pathTo/USeq/Apps/VCFBackgroundScanner -v SomaticVcfs/ -z 3
+-m bkg.mpileup.gz -s BkgFiltVcfs/ -b 1 -q 13 -e 
+
 **************************************************************************************
 </pre><br><p>
 				
@@ -4857,7 +4439,7 @@ <H1>Command Line Menus</H1> <p>
 </pre><br><p>
 				
 					<a name="VCFComparator"><pre>**************************************************************************************
-**                              VCF Comparator : June 2015                          **
+**                              VCF Comparator : Jan 2017                           **
 **************************************************************************************
 Compares test vcf file(s) against a gold standard key of trusted vcf calls. Only calls
 that fall in the common interrogated regions are compared. WARNING tabix gzipped files
@@ -4888,6 +4470,31 @@ <H1>Command Line Menus</H1> <p>
        -b /NIST/NA12878/regions.bed.gz -c /EdgeBio/Exome/testHaploCaller.vcf.zip
        -d /EdgeBio/Exome/NimbleGenExomeV3.bed -g -v -s -e -p /CompRes/ 
 
+**************************************************************************************
+</pre><br><p>
+				
+					<a name="VCFConsensus"><pre>**************************************************************************************
+**                              VCF Consensus : Jan 2016                            **
+**************************************************************************************
+Merges VCF files with the same #CHROM line. Primary records with the same chrPosRefAlt
+as a secondary are saved after appending the ID and FILTER, the secondary
+is dropped. Headers are joined keeping the primary header line when the same. Run
+iteratively with multiple VCF files you'd like to merge.  Good for combining multiple
+variant callers run on the same sample. The ID field lists which callers found each
+variant.
+
+Required:
+-p Path to a primary vcf file (xxx.vcf(.gz/.zip OK)) to merge.
+-s Path to a secondary vcf file (xxx.vcf(.gz/.zip OK)) to merge.
+-o Path to an output xxx.vcf.gz file.
+
+Optional:
+-q Primary name to replace the ID column.
+-t Secondary name to replace the ID column.
+
+Example: java -Xmx4G -jar pathTo/USeq/Apps/VCFConsensus -p illumina.vcf -q Strelka
+-s stnd.indel.vcf.gz -t Scalpel -o indelCalls.vcf.gz 
+
 **************************************************************************************
 </pre><br><p>
 				
@@ -5249,23 +4856,25 @@ <H1>Command Line Menus</H1> <p>
 </pre><br><p>
 				
 					<a name="StrelkaVCFParser"><pre>**************************************************************************************
-**                            Strelka VCF Parser: April 2016                        **
+**                             Strelka VCF Parser: Jan 2017                         **
 **************************************************************************************
 Parses Strelka VCF INDEL and SNV files, replacing the QUAl score with the QSI or QSS
-score. Also filters for minimum tumor normal read depth, T/N alt allelic ratio,
-and tumor and normal alt allelic ratios. Lastly, it sets the FILTER field to '.' and
-inserts the tumor DP and AF info.
+score. Also filters for read depth, T/N alt allelic ratio and diff,
+and tumor and normal alt allelic ratios. Lastly, it inserts the tumor DP and AF info.
 
 Required Params:
 -v Full path file or directory containing xxx.vcf(.gz/.zip OK) file(s).
 -m Minimum QSI or QSS score, defaults to 0.
--a Minimum alignment depth for both tumor and normal samples, defaults to 0.
--r Minimum alt Tum/Norm allelic ratio, defaults to 0.
--t Minimum tumor alt allelic fraction, defaults to 0.
--n Maximum normal alt allelic fraction, defaults to 1.
-
-Example: java -jar pathToUSeq/Apps/StrelkaVCFParser -v /VCFFiles/ -m 32 -a 150
-      -r 2 -n 0.6 -t 0.025  
+-t Minimum tumor allele frequency (AF), defaults to 0.
+-n Maximum normal AF, defaults to 1.
+-u Minimum tumor alignment depth, defaults to 0.
+-o Minimum normal alignment depth, defaults to 0.
+-d Minimum T-N AF difference, defaults to 0.
+-r Minimum T/N AF ratio, defaults to 0.
+-p Remove non PASS filter field records.
+
+Example: java -jar pathToUSeq/Apps/StrelkaVCFParser -v /VCFFiles/ -m 32 -t 0.05
+        -n 0.5 -u 100 -o 20 -d 0.05 -r 2
 
 **************************************************************************************
 </pre><br><p>
diff --git a/Source/edu/utah/seq/query/IndexRegion.java b/Source/edu/utah/seq/query/IndexRegion.java
new file mode 100644
index 00000000..13a22651
--- /dev/null
+++ b/Source/edu/utah/seq/query/IndexRegion.java
@@ -0,0 +1,31 @@
+package edu.utah.seq.query;
+
+
+public class IndexRegion implements Comparable<IndexRegion> {
+	protected int start;
+	protected int stop;
+	protected int fileId;
+	
+	public IndexRegion(int start, int stop, int fileId){
+		this.start = start;
+		this.stop = stop;
+		this.fileId = fileId;
+	}
+	
+	public String toString(){
+		return start+"-"+stop+"i"+fileId;
+	}
+	
+	/**Sorts by start base, then by stop, then fileId, smaller to larger for all.*/
+	public int compareTo(IndexRegion se){
+		if (start<se.start) return -1;
+		if (start>se.start) return 1;
+		//same start, sort by stop, smaller to larger
+		if (stop<se.stop) return -1;
+		if (stop>se.stop) return 1;
+		//same stop, sort by fileId, smaller to larger
+		if (fileId<se.fileId) return -1;
+		if (fileId>se.fileId) return 1;
+		return 0;
+	}
+}
\ No newline at end of file
diff --git a/Source/edu/utah/seq/query/QueryIndexFileLoader.java b/Source/edu/utah/seq/query/QueryIndexFileLoader.java
index c6d9c5ba..7b29335d 100644
--- a/Source/edu/utah/seq/query/QueryIndexFileLoader.java
+++ b/Source/edu/utah/seq/query/QueryIndexFileLoader.java
@@ -2,6 +2,7 @@
 
 import java.io.File;
 import java.io.IOException;
+import java.util.ArrayList;
 import java.util.regex.Matcher;
 import java.util.regex.Pattern;
 import htsjdk.tribble.readers.TabixReader;
@@ -19,6 +20,8 @@ public class QueryIndexFileLoader implements Runnable {
 	private File sourceFile = null;
 	private int indexLength = 0;
 	private boolean verbose;
+	private ArrayList<IndexRegion> toAdd = new ArrayList<IndexRegion>();
+	private static final int numToLoad = 2500;
 	
 	public static final Pattern END_POSITION = Pattern.compile(".*END=(\\d+).*", Pattern.CASE_INSENSITIVE);
 	
@@ -35,6 +38,8 @@ public void run() {
 			while ((sourceFile = queryIndexer.getFileToParse()) != null){ 
 				numPassed = 0;
 				numFailed = 0;
+				toAdd.clear();
+				int fileId = queryIndexer.getFileId().get(sourceFile);
 				
 				//fetch a reader and iterator on the entire chr
 				reader = new TabixReader(sourceFile.toString());
@@ -75,11 +80,11 @@ public void run() {
 						System.err.println("\tWARNING: This record's covered bps were trimmed ("+startStop[0]+" - "+startStop[1]+
 								") to match the chrom length ("+indexLength+") -> "+record);
 					}
-
-					//add in references to source file over the covered bases, stop isn't covered.
-					for (int j= startStop[0]; j< startStop[1]; j++) queryIndexer.addRef(j, sourceFile);
-
+					toAdd.add(new IndexRegion(startStop[0], startStop[1], fileId));
+					if (toAdd.size() > numToLoad) queryIndexer.addRegions(toAdd);
 				}
+				//add last
+				queryIndexer.addRegions(toAdd);
 				queryIndexer.incrementPassFail(numPassed, numFailed);
 				reader.close();
 			}	
diff --git a/Source/edu/utah/seq/query/QueryIndexer.java b/Source/edu/utah/seq/query/QueryIndexer.java
index efa09628..79701227 100644
--- a/Source/edu/utah/seq/query/QueryIndexer.java
+++ b/Source/edu/utah/seq/query/QueryIndexer.java
@@ -6,7 +6,6 @@
 import java.io.IOException;
 import java.io.PrintWriter;
 import java.util.ArrayList;
-import java.util.Arrays;
 import java.util.HashMap;
 import java.util.HashSet;
 import java.util.Iterator;
@@ -53,11 +52,11 @@ public class QueryIndexer {
 
 
 	//per chr fields
-	private TreeSet<File>[] workingIndex = null;
-	private HashMap<String, TreeSet<File>> fileNames2TheirPointers = new HashMap<String, TreeSet<File>>();
+	private ArrayList<IndexRegion>[] workingIndex = null;
 	private ArrayList<File> workingFilesToParse = null;
 	private long workingPassed = 0;
 	private long workingFailed = 0;
+	private String workingChr = null;
 
 	//constructor
 	@SuppressWarnings("unchecked")
@@ -75,7 +74,10 @@ public QueryIndexer(String[] args) {
 		//for each chromosome
 		if (verbose) System.out.println("Indexing records by chr...\n\tchr\t#pass\t#fail\tmemUsed");
 		else System.out.print("Indexing records by chr...\n\t"); 
-		for (String chr: chrLengths.keySet()) parseChr(chr);
+		for (String chr: chrLengths.keySet()) {
+			workingChr = chr;
+			parseChr();
+		}
 
 		if (verbose == false) System.out.println(": "+IO.memory());
 
@@ -86,14 +88,11 @@ public QueryIndexer(String[] args) {
 		System.out.println("Saving file headers...");
 		saveFileHeadersAndIds();
 
-		System.out.print("Building and saving interval trees...\n\t");
-		saveIntervalTrees();
-
 		String diffTime = Num.formatNumberOneFraction(((double)(System.currentTimeMillis() -startTime))/1000/60);
-		System.out.println("\n"+ diffTime+" Min to parse "+ totalRecordsProcessed+" records and build the query index trees");
+		System.out.println("\n"+ diffTime+" Min to parse "+ totalRecordsProcessed+" records and build the query index");
 	}
 
-	public void parseChr(String workingChr){
+	public void parseChr(){
 		try {
 			//any files?
 			workingFilesToParse = new ArrayList<File>();
@@ -105,7 +104,7 @@ public void parseChr(String workingChr){
 			if (workingFilesToParse.size() == 0) return; 
 
 			//prep for new chr
-			workingIndex = new TreeSet[chrLengths.get(workingChr)+1];
+			workingIndex = new ArrayList[chrLengths.get(workingChr)+1];
 			workingPassed = 0;
 			workingFailed = 0;
 
@@ -129,7 +128,7 @@ public void parseChr(String workingChr){
 			}
 
 			//save the index for this chrom
-			saveIndex(workingChr);
+			saveIndex();
 
 			//cleanup
 			if (verbose) System.out.println("\t"+workingChr+"\t"+workingPassed+"\t"+workingFailed+"\t"+IO.memory());
@@ -166,6 +165,21 @@ private void removeSkipDirs(ArrayList<File> al) {
 			e.printStackTrace();
 		} 
 	}
+	
+	synchronized void addRegions (ArrayList<IndexRegion> regions) {
+		for (IndexRegion region: regions){
+			//add start
+			int sIndex = region.start;
+			if (workingIndex[sIndex] == null) workingIndex[sIndex] = new ArrayList<IndexRegion>();
+			workingIndex[sIndex].add(region);
+
+			//add stop 
+			sIndex = region.stop;
+			if (workingIndex[sIndex] == null) workingIndex[sIndex] = new ArrayList<IndexRegion>();
+			workingIndex[sIndex].add(region);
+		}
+		regions.clear();
+	}
 
 	/**Gets a file to parse containing records that match a particular chr. Thread safe.*/
 	synchronized File getFileToParse(){
@@ -205,114 +219,43 @@ private void createFileIdHash() {
 		for (File f: dataFilesToParse) fileId.put(f, counter++);
 	}
 
-	public void saveIntervalTrees(){
-		try {
-			File[] chrBed = IO.extractFiles(indexDir, ".qi.bed.gz");
-			HashMap<String, IntervalST<int[]>> chrTrees = new HashMap<String, IntervalST<int[]>>();
-			HashMap<String, int[]> idsFileIndex = new HashMap<String, int[]>();
-			//for each file
-			for (File f: chrBed){
-				BufferedReader in = IO.fetchBufferedReader(f);
-				IntervalST<int[]> st = new IntervalST<int[]>();
-				String line;
-				while ((line = in.readLine())!= null){
-					String[] t = Misc.TAB.split(line);
-					int start = Integer.parseInt(t[1]);
-					int stop = Integer.parseInt(t[2]);
-					int[] ids = idsFileIndex.get(t[3]);
-					if (ids == null){
-						ids = stringToInts(t[3], Misc.COMMA);
-						idsFileIndex.put(t[3], ids);
-					}
-					//the end is included in IntervalST so sub 1 from end
-					st.put(new Interval1D(start, stop-1), ids);
-				}
-				in.close();
-
-				//save tree
-				String chr = f.getName().replace(".qi.bed.gz", "");
-
-				chrTrees.put(chr, st);
-				System.out.print(chr+" ");
-			}
-			System.out.println(": "+IO.memory());
-
-			File t = new File (indexDir, "its.obj");
-			IO.saveObject(t, chrTrees);
 
-		} catch (IOException e) {
-			e.printStackTrace();
-			Misc.printErrAndExit("\nERROR: problem saving interval trees, aborting.\n");
-		}
-	}
-
-	/**Given a String of ints delimited by something, will parse or return null.*/
-	public static int[] stringToInts(String s, Pattern pat){
-		String[] tokens = pat.split(s);
-		int[] num = new int[tokens.length];
-		try {
-			for (int i=0; i< tokens.length; i++){
-				num[i] = Integer.parseInt(tokens[i]);
-			}
-			return num;
-		} catch (Exception e){
-			return null;
-		}
-	}
-
-
-	public void saveIndex(String workingChr){
+	public void saveIndex(){
 		try {
 			File queryIndexFile = new File(indexDir, workingChr+".qi.bed");
 			PrintWriter out = new PrintWriter(new FileWriter((queryIndexFile)));
-			//collect bps with the same set of files
-			//start first entry, should always contain one or more files
-			int start = Integer.MIN_VALUE;
-			String priorIds = "";
-			int stop = Integer.MIN_VALUE;
-
+			HashSet<IndexRegion> openRegions = new HashSet<IndexRegion>();
+			int startPos = -1;
+			ArrayList<RegionToPrint> toSave = new ArrayList<RegionToPrint>();
+			
 			for (int i=0; i< workingIndex.length; i++){
-				if (workingIndex[i] == null) {
-					//in a block? write out old if not the first
-					if (start != Integer.MIN_VALUE){
-						out.print(workingChr); out.print("\t");
-						out.print(start); out.print("\t");
-						out.print(i); out.print("\t");
-						out.println(priorIds);
-
-						//reset start 
-						priorIds = "";
-						start = Integer.MIN_VALUE;
-					}
+				if (workingIndex[i]== null) continue;
+				//System.out.println(" xxxxxxxxxxxxxxxxxxxxxxxxxxxxx Index "+i);
+				
+				//first in block?
+				if (openRegions.size() == 0){
+					openRegions.addAll(workingIndex[i]);
+					startPos = i;
+					if (toSave.size() != 0) saveRegions(toSave, out);
 				}
-
-				//nope hash present
+				
+				//must be adding a new so need to save old
 				else {
-					//save last good position
-					stop = i;
-					//different ids?
-					String currentIds = fetchSortedIds(workingIndex[i]);
-					if (priorIds.equals(currentIds) == false){
-						//write out old if not the first
-						if (start != Integer.MIN_VALUE){
-							out.print(workingChr); out.print("\t");
-							out.print(start); out.print("\t");
-							out.print(stop); out.print("\t");
-							out.println(priorIds);
-						}
-						//start new
-						priorIds = currentIds;
-						start = i;
+					toSave.add(new RegionToPrint(startPos, i, fetchIds(openRegions)));
+					startPos = i;
+					
+					//go through each of the current index regions
+					for (IndexRegion ir: workingIndex[i]){
+						//already in open then this must be an end so remove it
+						if (openRegions.contains(ir)) openRegions.remove(ir);
+						//not present so this is a beginning, add it
+						else openRegions.add(ir);
 					}
 				}
 			}
 			//save last?
-			if (start != Integer.MIN_VALUE){
-				out.print(workingChr); out.print("\t");
-				out.print(start); out.print("\t");
-				out.print(stop+1); out.print("\t");
-				out.println(priorIds);
-			}
+			if (toSave.size() != 0) saveRegions(toSave, out);
+			
 			//close it
 			out.close();
 		} catch (IOException e){
@@ -320,75 +263,70 @@ public void saveIndex(String workingChr){
 			Misc.printErrAndExit("\nERROR: problem saving the index for "+workingChr+", aborting.\n");
 		}
 	}
-
-
-
-	/**Returns the int id concat rep for all the files in the sorted TreeSet*/
-	private String fetchSortedIds(TreeSet<File> files) {
-		int[] ids = new int[files.size()];
-		int counter = 0;
-		for (File f: files) ids[counter++] = fileId.get(f);
-		return Misc.intArrayToString(ids, ",");
-	}
-
-
-
-	/**Need to run through some gymnastics here since hits to the current TreeSet[] will be out of order and coming in from multiple threads.
-	 * Using this method as the bottleneck to keep the additions current. */
-	synchronized void addRef(int bp, File f) {
-
-		Integer fId = fileId.get(f);
-		//nothing entered just yet?
-		if (workingIndex[bp] == null) {
-			//any existing tree
-			TreeSet<File> ts = fileNames2TheirPointers.get(fId.toString());
-			if (ts == null){
-				ts = new TreeSet<File>();
-				ts.add(f);
-				fileNames2TheirPointers.put(fId.toString(), ts);
+	
+	private void saveRegions(ArrayList<RegionToPrint> al, PrintWriter out){
+		//set first
+		RegionToPrint rtp = al.get(0);
+		
+		//walk looking for same ids in following regions and merge em
+		int num = al.size();
+		for (int i=1; i< num; i++){
+			RegionToPrint next = al.get(i);
+			//same file id's
+			if (next.ids.equals(rtp.ids)) rtp.stop = next.stop;
+			else {
+				StringBuilder sb = new StringBuilder(workingChr);
+				rtp.appendInfo(sb);
+				out.println(sb);
+				rtp = next;
 			}
-			workingIndex[bp] = ts;
+		}
+		//print last
+		StringBuilder sb = new StringBuilder(workingChr);
+		rtp.appendInfo(sb);
+		out.println(sb);
+		al.clear();
+		
+	}
+	
+	private class RegionToPrint{
+		int start;
+		int stop;
+		String ids;
+		
+		public RegionToPrint(int start, int stop, String ids){
+			this.start = start;
+			this.stop = stop;
+			this.ids = ids;
 		}
 
-		//does the current hash already contain the file due to overlapping regions?
-		else if (workingIndex[bp].contains(f) == false){
-			//ok something there but it doesn't contain this file
-			//attempt to find an existing hash with these files
-			String key = fetchCompositeIdKey(workingIndex[bp], fId);
-			TreeSet<File> ts = fileNames2TheirPointers.get(key);
-			if (ts == null){
-				ts = new TreeSet<File>();
-				ts.addAll(workingIndex[bp]);
-				ts.add(f);
-				fileNames2TheirPointers.put(key, ts);
-			}
-			workingIndex[bp] = ts;
+		public void appendInfo(StringBuilder sb) {
+			sb.append("\t");
+			sb.append(start);
+			sb.append("\t");
+			sb.append(stop);
+			sb.append("\t");
+			sb.append(ids);
 		}
-		//yes, so don't do anything it's already there
 	}
 
-
-	/**This is expensive in computing time. Returns a String of sorted ints representing the file ids.*/
-	private String fetchCompositeIdKey(TreeSet<File> set, Integer newId) {
-		int numOld = set.size();
-
-		//make int[]
-		int[] ids = new int[numOld+1];
-		Iterator<File> it = set.iterator();
-		for (int i=0; i< numOld; i++) ids[i] = fileId.get(it.next());
-		ids[numOld] = newId;
-
-		//sort
-		Arrays.sort(ids);
-
-		//concat
-		StringBuilder sb = new StringBuilder();
-		sb.append(ids[0]);
-		for (int i=1; i< ids.length; i++){
+	private static String fetchIds(HashSet<IndexRegion> al) {
+		//just one?
+		if (al.size() == 1) return new Integer (al.iterator().next().fileId).toString();
+		
+		//hash ids and sort, might have dups
+		TreeSet<Integer> ids = new TreeSet<Integer>();
+		Iterator<IndexRegion> it = al.iterator();
+		while (it.hasNext())ids.add(it.next().fileId);
+	
+		//create string
+		Iterator<Integer>iit = ids.iterator();
+		StringBuilder sb = new StringBuilder(iit.next().toString());
+		while (iit.hasNext()){
 			sb.append(",");
-			sb.append(ids[i]);
+			sb.append(iit.next().toString());
 		}
-
+		
 		return sb.toString();
 	}
 
@@ -437,7 +375,7 @@ public void processArgs(String[] args){
 				try{
 					switch (test){
 					case 'c': chrNameLength = new File(args[++i]); break;
-					case 'd': dataDir = new File(args[++i]); break;
+					case 'd': dataDir = new File(args[++i]).getCanonicalFile(); break;
 					case 'i': indexDir = new File(args[++i]); break;
 					case 's': skipDirs = Misc.COMMA.split(args[++i]); break;
 					case 'q': verbose = false; break;
@@ -704,7 +642,7 @@ public static File[] returnFilesWithTabix(File[] tabixFiles) {
 	public static void printDocs(){
 		System.out.println("\n" +
 				"**************************************************************************************\n" +
-				"**                                Query Indexer: Dec 2016                           **\n" +
+				"**                                Query Indexer: Feb 2017                           **\n" +
 				"**************************************************************************************\n" +
 				"Builds index files for Query by recursing through a data directory looking for bgzip\n"+
 				"compressed and tabix indexed genomic data files (e.g. vcf, bed, maf, and custom).\n"+
@@ -747,7 +685,7 @@ public static void printDocs(){
 				"**************************************************************************************\n");
 	}
 
-	public TreeSet<File>[] getWorkingIndex() {
+	public ArrayList<IndexRegion>[] getWorkingIndex() {
 		return workingIndex;
 	}
 
@@ -755,4 +693,8 @@ public boolean isVerbose() {
 		return verbose;
 	}
 
+	public HashMap<File, Integer> getFileId() {
+		return fileId;
+	}
+
 }
diff --git a/Source/edu/utah/seq/vcf/VCFSample.java b/Source/edu/utah/seq/vcf/VCFSample.java
index e1c9fcbd..17de4666 100644
--- a/Source/edu/utah/seq/vcf/VCFSample.java
+++ b/Source/edu/utah/seq/vcf/VCFSample.java
@@ -36,7 +36,7 @@ public VCFSample(String sample, String sampleFormat) throws Exception{
 		this.originalRecord = sample;
 		this.originalFormat = sampleFormat;
 		//is it a no call?
-		if (sample.equals(".") || sample.equals("./.") ) noCall = true;
+		if (sample.equals(".") || sample.equals("./.") || sample.startsWith("./.:0,0") ) noCall = true;
 		else {
 			data = VCFParser.COLON.split(sample);
 			format = VCFParser.COLON.split(sampleFormat);
