From 4f3acda1ca8faed51a386c2d2edbd7e57a165415 Mon Sep 17 00:00:00 2001
From: Jeremy Goecks <jeremy.goecks@emory.edu>
Date: Thu, 9 May 2013 11:44:45 -0400
Subject: [PATCH] Visualization framework: replace summary_tree with bigwig
 datatype for all feature track coverage data, yielding better performance and
 a standardized approach for working with coverage data. Update Trackster to
 work with bigwig coverage data.

---
 datatypes_conf.xml.sample                     |  24 +-
 lib/galaxy/datatypes/binary.py                |   2 +-
 .../converters/bam_to_bigwig_converter.xml    |   9 +-
 .../bam_to_summary_tree_converter.xml         |  14 -
 .../bed_gff_or_vcf_to_bigwig_converter.xml    |  25 ++
 .../bed_to_summary_tree_converter.xml         |  14 -
 .../encodepeak_to_summary_tree_converter.xml  |  20 --
 .../gff_to_summary_tree_converter.xml         |  14 -
 .../interval_to_summary_tree_converter.py     |  63 -----
 .../interval_to_summary_tree_converter.xml    |  20 --
 .../sam_or_bam_to_summary_tree_converter.py   |  42 ---
 .../sam_to_summary_tree_converter.xml         |  14 -
 .../vcf_to_summary_tree_converter.py          |  30 ---
 .../vcf_to_summary_tree_converter.xml         |  14 -
 lib/galaxy/datatypes/interval.py              |  10 +-
 lib/galaxy/datatypes/tabular.py               |   4 +-
 .../visualization/data_providers/genome.py    |  74 ------
 .../visualization/data_providers/registry.py  |   1 -
 lib/galaxy/visualization/tracks/summary.py    | 117 ---------
 lib/galaxy/webapps/galaxy/api/datasets.py     |  49 ++--
 static/scripts/utils/config.js                |   1 -
 static/scripts/viz/trackster/painters.js      |  44 ----
 static/scripts/viz/trackster/tracks.js        | 246 +++++++++++-------
 static/scripts/viz/visualization.js           |   5 +-
 24 files changed, 227 insertions(+), 629 deletions(-)
 delete mode 100644 lib/galaxy/datatypes/converters/bam_to_summary_tree_converter.xml
 create mode 100644 lib/galaxy/datatypes/converters/bed_gff_or_vcf_to_bigwig_converter.xml
 delete mode 100644 lib/galaxy/datatypes/converters/bed_to_summary_tree_converter.xml
 delete mode 100644 lib/galaxy/datatypes/converters/encodepeak_to_summary_tree_converter.xml
 delete mode 100644 lib/galaxy/datatypes/converters/gff_to_summary_tree_converter.xml
 delete mode 100644 lib/galaxy/datatypes/converters/interval_to_summary_tree_converter.py
 delete mode 100644 lib/galaxy/datatypes/converters/interval_to_summary_tree_converter.xml
 delete mode 100644 lib/galaxy/datatypes/converters/sam_or_bam_to_summary_tree_converter.py
 delete mode 100644 lib/galaxy/datatypes/converters/sam_to_summary_tree_converter.xml
 delete mode 100644 lib/galaxy/datatypes/converters/vcf_to_summary_tree_converter.py
 delete mode 100644 lib/galaxy/datatypes/converters/vcf_to_summary_tree_converter.xml
 delete mode 100644 lib/galaxy/visualization/tracks/summary.py

diff --git a/datatypes_conf.xml.sample b/datatypes_conf.xml.sample
index 30c8fd0786c..b0d3481001f 100644
--- a/datatypes_conf.xml.sample
+++ b/datatypes_conf.xml.sample
@@ -9,12 +9,7 @@
     <datatype extension="fli" type="galaxy.datatypes.tabular:FeatureLocationIndex" display_in_upload="false"/>
     <datatype extension="bam" type="galaxy.datatypes.binary:Bam" mimetype="application/octet-stream" display_in_upload="true">
       <converter file="bam_to_bai.xml" target_datatype="bai"/>
-      <converter file="bam_to_summary_tree_converter.xml" target_datatype="summary_tree"/>
-      <!--
-        Caution: (a) this converter requires bedtools to be installed and (b) it is very memory intensive and
-        is not recommended for most laptops/desktops.
-        <converter file="bam_to_bigwig_converter.xml" target_datatype="bigwig"/>
-      -->
+      <converter file="bam_to_bigwig_converter.xml" target_datatype="bigwig"/>
       <display file="ucsc/bam.xml" />
       <display file="ensembl/ensembl_bam.xml" />
       <display file="igv/bam.xml" />
@@ -25,7 +20,7 @@
       <converter file="interval_to_coverage.xml" target_datatype="coverage"/>
       <converter file="bed_to_bgzip_converter.xml" target_datatype="bgzip"/>
       <converter file="bed_to_tabix_converter.xml" target_datatype="tabix" depends_on="bgzip"/>
-      <converter file="bed_to_summary_tree_converter.xml" target_datatype="summary_tree"/>
+      <converter file="bed_gff_or_vcf_to_bigwig_converter.xml" target_datatype="bigwig"/>
       <converter file="bed_to_fli_converter.xml" target_datatype="fli"/>
       <!-- <display file="ucsc/interval_as_bed.xml" /> -->
       <display file="igb/bed.xml" />
@@ -51,7 +46,7 @@
     <datatype extension="chrint" type="galaxy.datatypes.interval:ChromatinInteractions" display_in_upload="True">
       <converter file="interval_to_bgzip_converter.xml" target_datatype="bgzip"/>
       <converter file="interval_to_tabix_converter.xml" target_datatype="tabix" depends_on="bgzip"/>
-      <converter file="interval_to_summary_tree_converter.xml" target_datatype="summary_tree"/>
+      <converter file="bed_gff_or_vcf_to_bigwig_converter.xml" target_datatype="bigwig"/>
     </datatype>
     <!-- MSI added Datatypes -->
     <datatype extension="csv" type="galaxy.datatypes.tabular:Tabular" subclass="True" display_in_upload="true" /> <!-- FIXME: csv is 'tabular'ized data, but not 'tab-delimited'; the class used here is intended for 'tab-delimited' -->
@@ -93,7 +88,7 @@
     <datatype extension="gff" type="galaxy.datatypes.interval:Gff" display_in_upload="true">
       <converter file="gff_to_bed_converter.xml" target_datatype="bed"/>
       <converter file="gff_to_interval_index_converter.xml" target_datatype="interval_index"/>
-      <converter file="gff_to_summary_tree_converter.xml" target_datatype="summary_tree"/>
+      <converter file="bed_gff_or_vcf_to_bigwig_converter.xml" target_datatype="bigwig"/>
       <converter file="gff_to_fli_converter.xml" target_datatype="fli"/>
       <display file="ensembl/ensembl_gff.xml" inherit="True"/>
       <!-- <display file="gbrowse/gbrowse_gff.xml" inherit="True" /> -->
@@ -103,7 +98,7 @@
     <datatype extension="gmaj.zip" type="galaxy.datatypes.images:Gmaj" mimetype="application/zip"/>
     <datatype extension="gtf" type="galaxy.datatypes.interval:Gtf" display_in_upload="true">
         <converter file="gff_to_interval_index_converter.xml" target_datatype="interval_index"/>
-        <converter file="gff_to_summary_tree_converter.xml" target_datatype="summary_tree"/>
+        <converter file="bed_gff_or_vcf_to_bigwig_converter.xml" target_datatype="bigwig"/>
     </datatype>
     <datatype extension="toolshed.gz" type="galaxy.datatypes.binary:Binary" mimetype="multipart/x-gzip" subclass="True" />
     <datatype extension="h5" type="galaxy.datatypes.binary:Binary" mimetype="application/octet-stream" subclass="True" />
@@ -115,7 +110,7 @@
       <converter file="interval_to_bed12_converter.xml" target_datatype="bed12"/>
       <converter file="interval_to_bgzip_converter.xml" target_datatype="bgzip"/>
       <converter file="interval_to_tabix_converter.xml" target_datatype="tabix" depends_on="bgzip"/>
-	  <converter file="interval_to_summary_tree_converter.xml" target_datatype="summary_tree"/>
+	    <converter file="interval_to_bigwig_converter.xml" target_datatype="bigwig"/>
       <!-- <display file="ucsc/interval_as_bed.xml" inherit="True" /> -->
       <display file="ensembl/ensembl_interval_as_bed.xml" inherit="True"/>
       <display file="gbrowse/gbrowse_interval_as_bed.xml" inherit="True"/>
@@ -156,7 +151,7 @@
 	<datatype extension="encodepeak" type="galaxy.datatypes.interval:ENCODEPeak" display_in_upload="True">
 	  <converter file="encodepeak_to_tabix_converter.xml" target_datatype="tabix" depends_on="bgzip"/>
 	  <converter file="encodepeak_to_bgzip_converter.xml" target_datatype="bgzip"/>
-	  <converter file="encodepeak_to_summary_tree_converter.xml" target_datatype="summary_tree"/>
+	  <converter file="bed_gff_or_vcf_to_bigwig_converter.xml" target_datatype="bigwig"/>
 	</datatype>
     <datatype extension="pdf" type="galaxy.datatypes.images:Pdf" mimetype="application/pdf"/>
     <datatype extension="pileup" type="galaxy.datatypes.tabular:Pileup" display_in_upload="true">
@@ -172,7 +167,7 @@
     <datatype extension="Roadmaps" type="galaxy.datatypes.assembly:Roadmaps" display_in_upload="false"/>
     <datatype extension="sam" type="galaxy.datatypes.tabular:Sam" display_in_upload="true">
     	<converter file="sam_to_bam.xml" target_datatype="bam"/>
-    	<converter file="sam_to_summary_tree_converter.xml" target_datatype="summary_tree"/>
+    	<converter file="sam_to_bigwig_converter.xml" target_datatype="bigwig"/>
 	</datatype>
     <datatype extension="scf" type="galaxy.datatypes.binary:Scf" mimetype="application/octet-stream" display_in_upload="true"/>
     <datatype extension="Sequences" type="galaxy.datatypes.assembly:Sequences" display_in_upload="false"/>
@@ -190,7 +185,7 @@
       <converter file="vcf_to_bgzip_converter.xml" target_datatype="bgzip"/>
       <converter file="vcf_to_vcf_bgzip_converter.xml" target_datatype="vcf_bgzip"/>
       <converter file="vcf_to_tabix_converter.xml" target_datatype="tabix" depends_on="bgzip"/>
-      <converter file="vcf_to_summary_tree_converter.xml" target_datatype="summary_tree"/>
+      <converter file="bed_gff_or_vcf_to_bigwig_converter.xml" target_datatype="bigwig"/>
       <display file="ucsc/vcf.xml" />
       <display file="igv/vcf.xml" />
       <display file="rviewer/vcf.xml" inherit="True"/>
@@ -203,7 +198,6 @@
       <!-- <display file="gbrowse/gbrowse_wig.xml" /> -->
       <display file="igb/wig.xml" />
     </datatype>
-    <datatype extension="summary_tree" type="galaxy.datatypes.binary:Binary" subclass="True" />
     <datatype extension="interval_index" type="galaxy.datatypes.binary:Binary" subclass="True" />
     <datatype extension="tabix" type="galaxy.datatypes.binary:Binary" subclass="True" />
     <datatype extension="bgzip" type="galaxy.datatypes.binary:Binary" subclass="True" />
diff --git a/lib/galaxy/datatypes/binary.py b/lib/galaxy/datatypes/binary.py
index 5cbe223c81e..2a478d7f6df 100644
--- a/lib/galaxy/datatypes/binary.py
+++ b/lib/galaxy/datatypes/binary.py
@@ -103,7 +103,7 @@ class Bam( Binary ):
     """Class describing a BAM binary file"""
     file_ext = "bam"
     track_type = "ReadTrack"
-    data_sources = { "data": "bai", "index": [ "bigwig", "summary_tree" ] }
+    data_sources = { "data": "bai", "index": "bigwig" }
 
     MetadataElement( name="bam_index", desc="BAM Index File", param=metadata.FileParameter, file_ext="bai", readonly=True, no_value=None, visible=False, optional=True )
 
diff --git a/lib/galaxy/datatypes/converters/bam_to_bigwig_converter.xml b/lib/galaxy/datatypes/converters/bam_to_bigwig_converter.xml
index 739cca3d268..35f7b224083 100644
--- a/lib/galaxy/datatypes/converters/bam_to_bigwig_converter.xml
+++ b/lib/galaxy/datatypes/converters/bam_to_bigwig_converter.xml
@@ -1,7 +1,14 @@
 <tool id="CONVERTER_bam_to_bigwig_0" name="Convert BAM to BigWig" version="1.0.0" hidden="true">
     <!--  <description>__NOT_USED_CURRENTLY_FOR_CONVERTERS__</description> -->
     <command>
-        bedtools genomecov -bg -split -ibam $input -g $chromInfo | wigToBigWig stdin $chromInfo $output
+        bedtools genomecov -bg -split -ibam $input -g $chromInfo 
+
+        ## Streaming the bedgraph file to wigToBigWig is fast but very memory intensive; hence, this
+        ## should only be used on systems with large RAM.
+        ## | wigToBigWig stdin $chromInfo $output
+
+        ## This can be used anywhere.
+        > temp.bg ; bedGraphToBigWig temp.bg $chromInfo $output
     </command>
     <inputs>
         <param format="bam" name="input" type="data" label="Choose BAM file"/>
diff --git a/lib/galaxy/datatypes/converters/bam_to_summary_tree_converter.xml b/lib/galaxy/datatypes/converters/bam_to_summary_tree_converter.xml
deleted file mode 100644
index 5c05f020f56..00000000000
--- a/lib/galaxy/datatypes/converters/bam_to_summary_tree_converter.xml
+++ /dev/null
@@ -1,14 +0,0 @@
-<tool id="CONVERTER_bam_to_summary_tree_0" name="Convert BAM to Summary Tree" version="1.0.0" hidden="true">
-  <!--  <description>__NOT_USED_CURRENTLY_FOR_CONVERTERS__</description> -->
-  <command interpreter="python">
-    sam_or_bam_to_summary_tree_converter.py --bam $input1 $input1.metadata.bam_index $output1
-  </command>
-  <inputs>
-    <param format="bam" name="input1" type="data" label="Choose BAM file"/>
-   </inputs>
-  <outputs>
-    <data format="summary_tree" name="output1"/>
-  </outputs>
-  <help>
-  </help>
-</tool>
diff --git a/lib/galaxy/datatypes/converters/bed_gff_or_vcf_to_bigwig_converter.xml b/lib/galaxy/datatypes/converters/bed_gff_or_vcf_to_bigwig_converter.xml
new file mode 100644
index 00000000000..c0648f61481
--- /dev/null
+++ b/lib/galaxy/datatypes/converters/bed_gff_or_vcf_to_bigwig_converter.xml
@@ -0,0 +1,25 @@
+<tool id="CONVERTER_bed_gff_or_vcf_to_bigwig_0" name="Convert BED, GFF, or VCF to BigWig" version="1.0.0" hidden="true">
+    <!--  <description>__NOT_USED_CURRENTLY_FOR_CONVERTERS__</description> -->
+    <command>
+        ## Remove comments and sort by chromosome.
+        grep -v '^#' $input | sort -k1,1 | 
+
+        ## Generate coverage bedgraph.
+        bedtools genomecov -bg -split -i stdin -g $chromInfo 
+
+        ## Streaming the bedgraph file to wigToBigWig is fast but very memory intensive; hence, this
+        ## should only be used on systems with large RAM.
+        ## | wigToBigWig stdin $chromInfo $output
+
+        ## This can be used anywhere.
+        > temp.bg ; bedGraphToBigWig temp.bg $chromInfo $output
+    </command>
+    <inputs>
+        <param format="bed,gff,vcf" name="input" type="data" label="Choose input file"/>
+    </inputs>
+    <outputs>
+        <data format="bigwig" name="output"/>
+    </outputs>
+    <help>
+    </help>
+</tool>
diff --git a/lib/galaxy/datatypes/converters/bed_to_summary_tree_converter.xml b/lib/galaxy/datatypes/converters/bed_to_summary_tree_converter.xml
deleted file mode 100644
index b9067648f80..00000000000
--- a/lib/galaxy/datatypes/converters/bed_to_summary_tree_converter.xml
+++ /dev/null
@@ -1,14 +0,0 @@
-<tool id="CONVERTER_bed_to_summary_tree_0" name="Convert BED to Summary Tree" version="1.0.0" hidden="true">
-<!--  <description>__NOT_USED_CURRENTLY_FOR_CONVERTERS__</description> -->
-  <command interpreter="python">interval_to_summary_tree_converter.py $input1 $output1</command>
-  <inputs>
-    <page>
-        <param format="bed" name="input1" type="data" label="Choose BED file"/>
-    </page>
-   </inputs>
-  <outputs>
-    <data format="summary_tree" name="output1"/>
-  </outputs>
-  <help>
-  </help>
-</tool>
diff --git a/lib/galaxy/datatypes/converters/encodepeak_to_summary_tree_converter.xml b/lib/galaxy/datatypes/converters/encodepeak_to_summary_tree_converter.xml
deleted file mode 100644
index fc5db2e4bde..00000000000
--- a/lib/galaxy/datatypes/converters/encodepeak_to_summary_tree_converter.xml
+++ /dev/null
@@ -1,20 +0,0 @@
-<tool id="CONVERTER_encodepeak_to_summary_tree_0" name="Convert ENCODEPeak to Summary Tree" version="1.0.0" hidden="true">
-<!--  <description>__NOT_USED_CURRENTLY_FOR_CONVERTERS__</description> -->
-  <command interpreter="python">interval_to_summary_tree_converter.py 
-                                -c ${input1.metadata.chromCol} 
-                                -s ${input1.metadata.startCol} 
-                                -e ${input1.metadata.endCol} 
-                                $input1 $output1
-  </command>
-  
-  <inputs>
-    <page>
-        <param format="ENCODEPeak" name="input1" type="data" label="Choose ENCODEPeak file"/>
-    </page>
-   </inputs>
-  <outputs>
-    <data format="summary_tree" name="output1"/>
-  </outputs>
-  <help>
-  </help>
-</tool>
diff --git a/lib/galaxy/datatypes/converters/gff_to_summary_tree_converter.xml b/lib/galaxy/datatypes/converters/gff_to_summary_tree_converter.xml
deleted file mode 100644
index f61cdb6d90d..00000000000
--- a/lib/galaxy/datatypes/converters/gff_to_summary_tree_converter.xml
+++ /dev/null
@@ -1,14 +0,0 @@
-<tool id="CONVERTER_gff_to_summary_tree_0" name="Convert GFF to Summary Tree" version="1.0.0" hidden="true">
-<!--  <description>__NOT_USED_CURRENTLY_FOR_CONVERTERS__</description> -->
-  <command interpreter="python">interval_to_summary_tree_converter.py $input1 $output1 --gff</command>
-  <inputs>
-    <page>
-        <param format="gff" name="input1" type="data" label="Choose GFF file"/>
-    </page>
-   </inputs>
-  <outputs>
-    <data format="summary_tree" name="output1"/>
-  </outputs>
-  <help>
-  </help>
-</tool>
diff --git a/lib/galaxy/datatypes/converters/interval_to_summary_tree_converter.py b/lib/galaxy/datatypes/converters/interval_to_summary_tree_converter.py
deleted file mode 100644
index e61429f3eb5..00000000000
--- a/lib/galaxy/datatypes/converters/interval_to_summary_tree_converter.py
+++ /dev/null
@@ -1,63 +0,0 @@
-#!/usr/bin/env python
-
-"""
-Convert from interval file to summary tree file. Default input file format is BED (0-based, half-open intervals).
-
-usage: %prog <options> in_file out_file
-    -c, --chr-col: chromosome column, default=1
-    -s, --start-col: start column, default=2
-    -e, --end-col: end column, default=3
-    -t, --strand-col: strand column, default=6
-    -G, --gff: input is GFF format, meaning start and end coordinates are 1-based, closed interval
-"""
-from __future__ import division
-
-import sys, fileinput, optparse
-from galaxy import eggs
-import pkg_resources; pkg_resources.require( "bx-python" )
-from galaxy.visualization.tracks.summary import *
-from bx.intervals.io import *
-from galaxy.datatypes.util.gff_util import *
-
-def main():
-    # Read options, args.
-    parser = optparse.OptionParser()
-    parser.add_option( '-c', '--chr-col', type='int', dest='chrom_col', default=1 )
-    parser.add_option( '-s', '--start-col', type='int', dest='start_col', default=2 )
-    parser.add_option( '-e', '--end-col', type='int', dest='end_col', default=3 )
-    parser.add_option( '-t', '--strand-col', type='int', dest='strand_col', default=6 )
-    parser.add_option( '-G', '--gff', dest="gff_format", action="store_true" )
-    (options, args) = parser.parse_args()
-    input_fname, output_fname = args
-    
-    # Convert column indices to 0-based.
-    options.chrom_col -= 1
-    options.start_col -= 1
-    options.end_col -= 1
-    options.strand_col -= 1
-        
-    # Do conversion.
-    if options.gff_format:
-        reader_wrapper_class = GFFReaderWrapper
-        chr_col, start_col, end_col, strand_col = ( 0, 3, 4, 6 )
-    else:
-        reader_wrapper_class = NiceReaderWrapper
-        chr_col, start_col, end_col, strand_col = ( options.chrom_col, options.start_col, options.end_col, options.strand_col )
-    reader_wrapper = reader_wrapper_class( fileinput.FileInput( input_fname ),
-                                            chrom_col=chr_col,
-                                            start_col=start_col,
-                                            end_col=end_col,
-                                            strand_col=strand_col,
-                                            fix_strand=True )
-    st = SummaryTree()
-    for feature in list( reader_wrapper ):
-        if isinstance( feature, GenomicInterval ):
-            # Tree expects BED coordinates.
-            if type( feature ) is GFFFeature:
-                convert_gff_coords_to_bed( feature )
-            st.insert_range( feature.chrom, long( feature.start ), long( feature.end ) )
-    
-    st.write( output_fname )
-
-if __name__ == "__main__": 
-    main()
diff --git a/lib/galaxy/datatypes/converters/interval_to_summary_tree_converter.xml b/lib/galaxy/datatypes/converters/interval_to_summary_tree_converter.xml
deleted file mode 100644
index 103c7fa4d16..00000000000
--- a/lib/galaxy/datatypes/converters/interval_to_summary_tree_converter.xml
+++ /dev/null
@@ -1,20 +0,0 @@
-<tool id="CONVERTER_interval_to_summary_tree_0" name="Convert Interval to Summary Tree" version="1.0.0" hidden="true">
-<!--  <description>__NOT_USED_CURRENTLY_FOR_CONVERTERS__</description> -->
-  <command interpreter="python">interval_to_summary_tree_converter.py 
-                                -c ${input1.metadata.chromCol} 
-                                -s ${input1.metadata.startCol} 
-                                -e ${input1.metadata.endCol} 
-                                $input1 $output1
-  </command>
-  
-  <inputs>
-    <page>
-        <param format="interval" name="input1" type="data" label="Choose Interval file"/>
-    </page>
-   </inputs>
-  <outputs>
-    <data format="summary_tree" name="output1"/>
-  </outputs>
-  <help>
-  </help>
-</tool>
diff --git a/lib/galaxy/datatypes/converters/sam_or_bam_to_summary_tree_converter.py b/lib/galaxy/datatypes/converters/sam_or_bam_to_summary_tree_converter.py
deleted file mode 100644
index 951fac7f88b..00000000000
--- a/lib/galaxy/datatypes/converters/sam_or_bam_to_summary_tree_converter.py
+++ /dev/null
@@ -1,42 +0,0 @@
-#!/usr/bin/env python
-
-from __future__ import division
-
-import sys, os, optparse
-sys.stderr = open(os.devnull, 'w')  # suppress stderr as cython produces warning on some systems:
-                                    # csamtools.so:6: RuntimeWarning: __builtin__.file size changed
-
-from galaxy import eggs
-import pkg_resources
-
-if sys.version_info[:2] == (2, 4):
-    pkg_resources.require( "ctypes" )
-pkg_resources.require( "pysam" )
-
-from pysam import csamtools
-from galaxy.visualization.tracks.summary import *
-
-def main():
-    parser = optparse.OptionParser()
-    parser.add_option( '-S', '--sam', action="store_true", dest="is_sam" )
-    parser.add_option( '-B', '--bam', action="store_true", dest="is_bam" )
-    options, args = parser.parse_args()
-    
-    if options.is_bam:
-        input_fname = args[0]
-        index_fname = args[1]
-        out_fname = args[2]
-        samfile = csamtools.Samfile( filename=input_fname, mode='rb', index_filename=index_fname )
-    elif options.is_sam:
-        input_fname = args[0]
-        out_fname = args[1]
-        samfile = csamtools.Samfile( filename=input_fname, mode='r' )
-    
-    st = SummaryTree()
-    for read in samfile.fetch():
-        st.insert_range( samfile.getrname( read.rname ), read.pos, read.pos + read.rlen )
-    
-    st.write(out_fname)
-
-if __name__ == "__main__": 
-    main()
diff --git a/lib/galaxy/datatypes/converters/sam_to_summary_tree_converter.xml b/lib/galaxy/datatypes/converters/sam_to_summary_tree_converter.xml
deleted file mode 100644
index 6dd1c50ac05..00000000000
--- a/lib/galaxy/datatypes/converters/sam_to_summary_tree_converter.xml
+++ /dev/null
@@ -1,14 +0,0 @@
-<tool id="CONVERTER_sam_to_summary_tree_0" name="Convert SAM to Summary Tree" version="1.0.0" hidden="true">
-<!--  <description>__NOT_USED_CURRENTLY_FOR_CONVERTERS__</description> -->
-  <command interpreter="python">sam_or_bam_to_summary_tree_converter.py --sam $input1 $output1</command>
-  <inputs>
-    <page>
-        <param format="sam" name="input1" type="data" label="Choose sam file"/>
-    </page>
-   </inputs>
-  <outputs>
-    <data format="summary_tree" name="output1"/>
-  </outputs>
-  <help>
-  </help>
-</tool>
diff --git a/lib/galaxy/datatypes/converters/vcf_to_summary_tree_converter.py b/lib/galaxy/datatypes/converters/vcf_to_summary_tree_converter.py
deleted file mode 100644
index e46ddf7ca76..00000000000
--- a/lib/galaxy/datatypes/converters/vcf_to_summary_tree_converter.py
+++ /dev/null
@@ -1,30 +0,0 @@
-#!/usr/bin/env python
-
-"""
-Convert from VCF file to summary tree file.
-
-usage: %prog in_file out_file
-"""
-from __future__ import division
-
-import optparse
-import galaxy_utils.sequence.vcf
-from galaxy.visualization.tracks.summary import SummaryTree
-
-def main():
-    # Read options, args.
-    parser = optparse.OptionParser()
-    (options, args) = parser.parse_args()
-    in_file, out_file = args
-        
-    # Do conversion.
-    st = SummaryTree()
-    for line in list( galaxy_utils.sequence.vcf.Reader( open( in_file ) ) ):
-        # VCF format provides a chrom and 1-based position for each variant. 
-        # SummaryTree expects 0-based coordinates.
-        st.insert_range( line.chrom, long( line.pos-1 ), long( line.pos ) )
-    
-    st.write(out_file)
-
-if __name__ == "__main__": 
-    main()
\ No newline at end of file
diff --git a/lib/galaxy/datatypes/converters/vcf_to_summary_tree_converter.xml b/lib/galaxy/datatypes/converters/vcf_to_summary_tree_converter.xml
deleted file mode 100644
index 1217b8afffb..00000000000
--- a/lib/galaxy/datatypes/converters/vcf_to_summary_tree_converter.xml
+++ /dev/null
@@ -1,14 +0,0 @@
-<tool id="CONVERTER_vcf_to_summary_tree_0" name="Convert VCF to Summary Tree" version="1.0.0" hidden="true">
-  <!-- <description>__NOT_USED_CURRENTLY_FOR_CONVERTERS__</description> -->
-  <command interpreter="python">vcf_to_summary_tree_converter.py $input1 $output1</command>
-  <inputs>
-    <page>
-        <param format="vcf" name="input1" type="data" label="Choose VCF file"/>
-    </page>
-   </inputs>
-  <outputs>
-    <data format="summary_tree" name="output1"/>
-  </outputs>
-  <help>
-  </help>
-</tool>
diff --git a/lib/galaxy/datatypes/interval.py b/lib/galaxy/datatypes/interval.py
index f564e2e041c..f6e14e31fd3 100644
--- a/lib/galaxy/datatypes/interval.py
+++ b/lib/galaxy/datatypes/interval.py
@@ -47,7 +47,7 @@ class Interval( Tabular ):
     file_ext = "interval"
     line_class = "region"
     track_type = "FeatureTrack"
-    data_sources = { "data": "tabix", "index": "summary_tree" }
+    data_sources = { "data": "tabix", "index": "bigwig" }
 
     """Add metadata elements"""
     MetadataElement( name="chromCol", default=1, desc="Chrom column", param=metadata.ColumnParameter )
@@ -354,7 +354,7 @@ class BedGraph( Interval ):
 class Bed( Interval ):
     """Tab delimited data in BED format"""
     file_ext = "bed"
-    data_sources = { "data": "tabix", "index": "summary_tree", "feature_search": "fli" }
+    data_sources = { "data": "tabix", "index": "bigwig", "feature_search": "fli" }
     track_type = Interval.track_type
 
     """Add metadata elements"""
@@ -569,7 +569,7 @@ class Gff( Tabular, _RemoteCallMixin ):
     """Tab delimited data in Gff format"""
     file_ext = "gff"
     column_names = [ 'Seqname', 'Source', 'Feature', 'Start', 'End', 'Score', 'Strand', 'Frame', 'Group' ]
-    data_sources = { "data": "interval_index", "index": "summary_tree", "feature_search": "fli" }
+    data_sources = { "data": "interval_index", "index": "bigwig", "feature_search": "fli" }
     track_type = Interval.track_type
 
     """Add metadata elements"""
@@ -1288,7 +1288,7 @@ class ENCODEPeak( Interval ):
     
     file_ext = "encodepeak"
     column_names = [ 'Chrom', 'Start', 'End', 'Name', 'Score', 'Strand', 'SignalValue', 'pValue', 'qValue', 'Peak' ]
-    data_sources = { "data": "tabix", "index": "summary_tree" }
+    data_sources = { "data": "tabix", "index": "bigwig" }
     
     """Add metadata elements"""
     MetadataElement( name="chromCol", default=1, desc="Chrom column", param=metadata.ColumnParameter )
@@ -1307,7 +1307,7 @@ class ChromatinInteractions( Interval ):
     
     file_ext = "chrint"
     track_type = "DiagonalHeatmapTrack"
-    data_sources = { "data": "tabix", "index": "summary_tree" }
+    data_sources = { "data": "tabix", "index": "bigwig" }
     
     column_names = [ 'Chrom1', 'Start1', 'End1', 'Chrom2', 'Start2', 'End2', 'Value' ]
     
diff --git a/lib/galaxy/datatypes/tabular.py b/lib/galaxy/datatypes/tabular.py
index 8d0559a1526..c8858c61472 100644
--- a/lib/galaxy/datatypes/tabular.py
+++ b/lib/galaxy/datatypes/tabular.py
@@ -359,7 +359,7 @@ class Taxonomy( Tabular ):
 class Sam( Tabular ):
     file_ext = 'sam'
     track_type = "ReadTrack"
-    data_sources = { "data": "bam", "index": "summary_tree" }
+    data_sources = { "data": "bam", "index": "bigwig" }
 
     def __init__(self, **kwd):
         """Initialize taxonomy datatype"""
@@ -537,7 +537,7 @@ class ElandMulti( Tabular ):
 class Vcf( Tabular ):
     """ Variant Call Format for describing SNPs and other simple genome variations. """
     track_type = "VariantTrack"
-    data_sources = { "data": "tabix", "index": "summary_tree" }
+    data_sources = { "data": "tabix", "index": "bigwig" }
 
     file_ext = 'vcf'
     column_names = [ 'Chrom', 'Pos', 'ID', 'Ref', 'Alt', 'Qual', 'Filter', 'Info', 'Format', 'data' ]
diff --git a/lib/galaxy/visualization/data_providers/genome.py b/lib/galaxy/visualization/data_providers/genome.py
index b3e073dcf21..6a54633c8d6 100644
--- a/lib/galaxy/visualization/data_providers/genome.py
+++ b/lib/galaxy/visualization/data_providers/genome.py
@@ -14,7 +14,6 @@ from galaxy.util.json import from_json_string
 from bx.interval_index_file import Indexes
 from bx.bbi.bigwig_file import BigWigFile
 from galaxy.util.lrucache import LRUCache
-from galaxy.visualization.tracks.summary import summary_tree_from_file
 from galaxy.visualization.data_providers.basic import BaseDataProvider
 from galaxy.visualization.data_providers.cigar import get_ref_based_read_seq_and_cigar
 from galaxy.datatypes.interval import Bed, Gff, Gtf
@@ -800,79 +799,6 @@ class RawVcfDataProvider( VcfDataProvider ):
         
         return line_filter_iter()
 
-class SummaryTreeDataProvider( GenomeDataProvider ):
-    """
-    Summary tree data provider for the Galaxy track browser. 
-    """
-
-    dataset_type = 'summary_tree'
-    
-    CACHE = LRUCache( 20 ) # Store 20 recently accessed indices for performance
-    
-    def valid_chroms( self ):
-        st = summary_tree_from_file( self.converted_dataset.file_name )
-        return st.chrom_blocks.keys()
-    
-    def get_data( self, chrom, start, end, level=None, resolution=None, detail_cutoff=None, draw_cutoff=None, **kwargs ):
-        """
-        Returns summary tree data for a given genomic region.
-        """
-        filename = self.converted_dataset.file_name
-        st = self.CACHE[filename]
-        if st is None:
-            st = summary_tree_from_file( self.converted_dataset.file_name )
-            self.CACHE[filename] = st
-
-        # Look for chrom in tree using both naming conventions.
-        if chrom not in st.chrom_blocks:
-            chrom = _convert_between_ucsc_and_ensemble_naming( chrom )
-            if chrom not in st.chrom_blocks:
-                return None
-
-        # Get or compute level.
-        if level:
-            level = int( level )
-        elif resolution:
-            resolution = max( 1, ceil( float( resolution ) ) )
-            level = ceil( log( resolution, st.block_size ) ) - 1
-            level = int( max( level, 0 ) )
-        else:
-            # Either level or resolution is required.
-            return None
-
-        if level <= 1:
-            return "detail"
-
-        # Use level to get results.
-        stats = st.chrom_stats[ chrom ]
-        results = st.query( chrom, int(start), int(end), level, detail_cutoff=detail_cutoff, draw_cutoff=draw_cutoff )
-        if results == "detail" or results == "draw":
-            return results
-        else:
-            return {
-                'dataset_type': self.dataset_type,
-                'data': results,
-                'max': stats[ level ][ "max" ],
-                'avg': stats[ level ][ "avg" ],
-                'delta': stats[ level ][ "delta" ],
-                'level': level
-            }
-            
-    def has_data( self, chrom ):
-        """
-        Returns true if dataset has data for this chrom
-        """
-        
-        # Get summary tree.
-        filename = self.converted_dataset.file_name
-        st = self.CACHE[filename]
-        if st is None:
-            st = summary_tree_from_file( self.converted_dataset.file_name )
-            self.CACHE[filename] = st
-            
-        # Check for data.
-        return st.chrom_blocks.get(chrom, None) or st.chrom_blocks.get(_convert_between_ucsc_and_ensemble_naming(chrom), None)
-
 class BamDataProvider( GenomeDataProvider, FilterableMixin ):
     """
     Provides access to intervals from a sorted indexed BAM file. Coordinate 
diff --git a/lib/galaxy/visualization/data_providers/registry.py b/lib/galaxy/visualization/data_providers/registry.py
index 797b3f4a57c..a86cd73a2cd 100644
--- a/lib/galaxy/visualization/data_providers/registry.py
+++ b/lib/galaxy/visualization/data_providers/registry.py
@@ -29,7 +29,6 @@ class DataProviderRegistry( object ):
             "interval_index": genome.IntervalIndexDataProvider,
             "bai": genome.BamDataProvider,
             "bam": genome.SamDataProvider,
-            "summary_tree": genome.SummaryTreeDataProvider,
             "bigwig": genome.BigWigDataProvider,
             "bigbed": genome.BigBedDataProvider
         }
diff --git a/lib/galaxy/visualization/tracks/summary.py b/lib/galaxy/visualization/tracks/summary.py
deleted file mode 100644
index 801fb37ed87..00000000000
--- a/lib/galaxy/visualization/tracks/summary.py
+++ /dev/null
@@ -1,117 +0,0 @@
-'''
-This module cannot be moved due to the use of pickling.
-'''
-
-import sys, os
-import cPickle
-
-# TODO: What are the performance implications of setting min level to 1? Data
-# structure size and/or query speed? It would be nice to have level 1 data
-# so that client does not have to compute it.
-MIN_LEVEL = 2
-
-class SummaryTree:
-    '''
-    Summary tree data structure for feature aggregation across large genomic regions.
-    '''
-    def __init__( self, block_size=25, levels=6, draw_cutoff=150, detail_cutoff=30 ):
-        self.chrom_blocks = {}
-        self.levels = levels
-        self.draw_cutoff = draw_cutoff
-        self.detail_cutoff = detail_cutoff
-        self.block_size = block_size
-        self.chrom_stats = {}
-    
-    def find_block( self, num, level ):
-        """ Returns block that num is in for level. """
-        return ( num / self.block_size ** level )
-        
-    def insert_range( self, chrom, start, end ):
-        """ Inserts a feature at chrom:start-end into the tree. """
-        
-        # Get or set up chrom blocks.
-        if chrom in self.chrom_blocks:
-            blocks = self.chrom_blocks[ chrom ]
-        else:
-            blocks = self.chrom_blocks[ chrom ] = {}
-            self.chrom_stats[ chrom ] = {}
-            for level in range( MIN_LEVEL, self.levels + 1 ):
-                blocks[ level ] = {}
-            
-        # Insert feature into all matching blocks at all levels.
-        for level in range( MIN_LEVEL, self.levels + 1 ):
-            block_level = blocks[ level ]
-            starting_block = self.find_block( start, level )
-            ending_block = self.find_block( end, level )
-            for block in range( starting_block, ending_block + 1 ):
-                if block in block_level:
-                    block_level[ block ] += 1
-                else:
-                    block_level[ block ] = 1
-        
-    def finish( self ):
-        """ Compute stats for levels. """
-        
-        for chrom, blocks in self.chrom_blocks.iteritems():
-            for level in range( self.levels, MIN_LEVEL - 1, -1 ):
-                # Set level's stats.
-                max_val = max( blocks[ level ].values() )
-                self.chrom_stats[ chrom ][ level ] = {}
-                self.chrom_stats[ chrom ][ level ][ "delta" ] = self.block_size ** level
-                self.chrom_stats[ chrom ][ level ][ "max" ] = max_val
-                self.chrom_stats[ chrom ][ level ][ "avg" ] = float( max_val ) / len( blocks[ level ] )
-            
-            self.chrom_blocks[ chrom ] = dict( [ ( key, value ) for key, value in blocks.iteritems() ] )
-        
-    def query( self, chrom, start, end, level, draw_cutoff=None, detail_cutoff=None ):
-        """ Queries tree for data. """
-
-        # Set cutoffs to self's attributes if not defined.
-        if draw_cutoff != 0:
-            draw_cutoff = self.draw_cutoff
-        if detail_cutoff != 0:
-            detail_cutoff = self.detail_cutoff
-
-        # Get data.
-        if chrom in self.chrom_blocks:
-            stats = self.chrom_stats[ chrom ]
-
-            # For backwards compatibility:
-            if "detail_level" in stats and level <= stats[ "detail_level" ]:
-                return "detail"
-            elif "draw_level" in stats and level <= stats[ "draw_level" ]:
-                return "draw"
-
-            # If below draw, detail level, return string to denote this.
-            max = stats[ level ][ "max" ]
-            if max < detail_cutoff:
-                return "detail"
-            if max < draw_cutoff:
-                return "draw"
-            
-            # Return block data.
-            blocks = self.chrom_blocks[ chrom ]
-            results = []
-            multiplier = self.block_size ** level
-            starting_block = self.find_block( start, level )
-            ending_block = self.find_block( end, level )
-            for block in range( starting_block, ending_block + 1 ):
-                val = 0
-                if block in blocks[ level ]:
-                    val = blocks[ level ][ block ]
-                results.append(  ( block * multiplier, val )  )
-            return results
-            
-        return None
-        
-    def write( self, filename ):
-        """ Writes tree to file. """
-        self.finish()
-        cPickle.dump( self, open( filename, 'wb' ), 2 )
-        
-def summary_tree_from_file( filename ):
-    st_file = open( filename, "rb" )
-    st = cPickle.load( st_file )
-    st_file.close()
-    return st
-    
diff --git a/lib/galaxy/webapps/galaxy/api/datasets.py b/lib/galaxy/webapps/galaxy/api/datasets.py
index 6d66328c198..8e38f85fce8 100644
--- a/lib/galaxy/webapps/galaxy/api/datasets.py
+++ b/lib/galaxy/webapps/galaxy/api/datasets.py
@@ -145,32 +145,41 @@ class DatasetsController( BaseAPIController, UsesVisualizationMixin, UsesHistory
             
         extra_info = None
         mode = kwargs.get( "mode", "Auto" )
-        # Handle histogram mode uniquely for now:
         data_provider_registry = trans.app.data_provider_registry
+
+        # Coverage mode uses index data.
         if mode == "Coverage":
             # Get summary using minimal cutoffs.
             indexer = data_provider_registry.get_data_provider( trans, original_dataset=dataset, source='index' )
-            summary = indexer.get_data( chrom, low, high, detail_cutoff=0, draw_cutoff=0, **kwargs )
-            if summary == "detail":
-                # Use maximum level of detail--2--to get summary data no matter the resolution.
-                summary = indexer.get_data( chrom, low, high, resolution=kwargs[ 'resolution' ],
-                                            level=2, detail_cutoff=0, draw_cutoff=0 )
-            return summary
+            return indexer.get_data( chrom, low, high, **kwargs )
 
-        if 'index' in data_sources and data_sources['index']['name'] == "summary_tree" and mode == "Auto":
-            # Only check for summary_tree if it's Auto mode (which is the default)
-            # 
-            # Have to choose between indexer and data provider
+        # TODO: 
+        # (1) add logic back in for no_detail
+        # (2) handle scenario where mode is Squish/Pack but data requested is large, so reduced data needed to be returned.
+            
+        # If mode is Auto, need to determine what type of data to return.
+        if mode == "Auto":
+            # Get stats from indexer.
             indexer = data_provider_registry.get_data_provider( trans, original_dataset=dataset, source='index' )
-            summary = indexer.get_data( chrom, low, high, resolution=kwargs[ 'resolution' ] )
-            if summary is None:
-                return { 'dataset_type': indexer.dataset_type, 'data': None }
-                
-            if summary == "draw":
-                kwargs["no_detail"] = True # meh
-                extra_info = "no_detail"
-            elif summary != "detail":
-                return summary
+            stats = indexer.get_data( chrom, low, high, stats=True )
+
+            # If stats were requested, return them.
+            if 'stats' in kwargs:
+                if stats[ 'data' ][ 'max' ] == 0:
+                    return { 'dataset_type': indexer.dataset_type, 'data': None }
+                else:
+                    return stats
+
+            # Use heuristic based on max depth and region size to determine whether to 
+            # return coverage data. When zoomed out and region is large, max depth
+            # is determining factor. However, when sufficiently zoomed in and region is 
+            # small, coverage data is no longer provided.
+            if int( high ) - int( low ) > 50000 and stats[ 'data' ][ 'max' ] > 1000:
+                return indexer.get_data( chrom, low, high )
+ 
+        #
+        # Provide individual data points.
+        #
         
         # Get data provider.
         data_provider = data_provider_registry.get_data_provider( trans, original_dataset=dataset, source='data' )
diff --git a/static/scripts/utils/config.js b/static/scripts/utils/config.js
index a35ddd7ce47..7a79a412dc8 100644
--- a/static/scripts/utils/config.js
+++ b/static/scripts/utils/config.js
@@ -58,7 +58,6 @@ var ConfigSetting = Backbone.Model.extend({
         { key: 'mode', type: 'string', default_value: this.mode, hidden: true },
         { key: 'reverse_strand_color', label: 'Antisense strand color', type: 'color', default_value: null },
         { key: 'show_differences', label: 'Show differences only', type: 'bool', default_value: true },
-        { key: 'histogram_max', label: 'Histogram maximum', type: 'float', default_value: null, help: 'Clear value to set automatically' },
         { key: 'mode', type: 'string', default_value: this.mode, hidden: true }
     ]
 });
diff --git a/static/scripts/viz/trackster/painters.js b/static/scripts/viz/trackster/painters.js
index d7608e51bdf..69a0783e0f2 100644
--- a/static/scripts/viz/trackster/painters.js
+++ b/static/scripts/viz/trackster/painters.js
@@ -133,49 +133,6 @@ Painter.prototype.default_prefs = {};
  */
 Painter.prototype.draw = function(ctx, width, height, w_scale) {};
 
-/**
- * SummaryTreePainter, a histogram showing number of intervals in a region
- */
-var SummaryTreePainter = function(data, view_start, view_end, prefs, mode) {
-    Painter.call(this, data, view_start, view_end, prefs, mode);
-};
-
-SummaryTreePainter.prototype.default_prefs = { show_counts: false };
-
-SummaryTreePainter.prototype.draw = function(ctx, width, height, w_scale) {
-    var view_start = this.view_start,
-        points = this.data.data,
-        max = (this.prefs.histogram_max ? this.prefs.histogram_max : this.data.max),
-        // Set base Y so that max label and data do not overlap. Base Y is where rectangle bases
-        // start. However, height of each rectangle is relative to required_height; hence, the
-        // max rectangle is required_height.
-        base_y = height,
-        delta_x_px = Math.ceil(this.data.delta * w_scale);
-    ctx.save();
-    
-    for (var i = 0, len = points.length; i < len; i++) {
-        var x = Math.floor( (points[i][0] - view_start) * w_scale );
-        var y = points[i][1];
-        
-        if (!y) { continue; }
-        var y_px = y / max * height;
-        if (y !== 0 && y_px < 1) { y_px = 1; }
-
-        ctx.fillStyle = this.prefs.block_color;
-        ctx.fillRect( x, base_y - y_px, delta_x_px, y_px );
-        
-        // Draw number count if it can fit the number with some padding, otherwise things clump up
-        var text_padding_req_x = 4;
-        if (this.prefs.show_counts && (ctx.measureText(y).width + text_padding_req_x) < delta_x_px) {
-            ctx.fillStyle = this.prefs.label_color;
-            ctx.textAlign = "center";
-            ctx.fillText(y, x + (delta_x_px/2), 10);
-        }
-    }
-    
-    ctx.restore();
-};
-
 var LinePainter = function(data, view_start, view_end, prefs, mode) {
     Painter.call( this, data, view_start, view_end, prefs, mode );
     var i, len;
@@ -1692,7 +1649,6 @@ extend(VariantPainter.prototype, Painter.prototype, {
 
 return {
     Scaler: Scaler,
-    SummaryTreePainter: SummaryTreePainter,
     LinePainter: LinePainter,
     LinkedFeaturePainter: LinkedFeaturePainter,
     ReadPainter: ReadPainter,
diff --git a/static/scripts/viz/trackster/tracks.js b/static/scripts/viz/trackster/tracks.js
index 05bece4d0d5..79f6f33121f 100644
--- a/static/scripts/viz/trackster/tracks.js
+++ b/static/scripts/viz/trackster/tracks.js
@@ -2076,11 +2076,10 @@ var Tile = function(track, region, resolution, canvas, data) {
  */
 Tile.prototype.predisplay_actions = function() {};
 
-var SummaryTreeTile = function(track, region, resolution, canvas, data, max_val) {
+var LineTrackTile = function(track, region, resolution, canvas, data) {
     Tile.call(this, track, region, resolution, canvas, data);
-    this.max_val = max_val;
 };
-extend(SummaryTreeTile.prototype, Tile.prototype);
+LineTrackTile.prototype.predisplay_actions = function() {};
 
 var FeatureTrackTile = function(track, region, resolution, canvas, data, w_scale, mode, message, all_slotted, feature_mapper) {
     // Attribute init.
@@ -2601,7 +2600,7 @@ extend(Track.prototype, Drawable.prototype, {
         track.enabled = false;
         track.tile_cache.clear();    
         track.data_manager.clear();
-        track.content_div.css("height", "auto");
+        track.tiles_div.css("height", "auto");
         /*
         if (!track.content_div.text()) {
             track.content_div.text(DATA_LOADING);
@@ -2669,7 +2668,7 @@ extend(Track.prototype, Drawable.prototype, {
                     track.tiles_div.css( "height", track.visible_height_px + "px" );
                     track.enabled = true;
                     // predraw_init may be asynchronous, wait for it and then draw
-                    $.when(track.predraw_init()).done(function() {
+                    $.when.apply($, track.predraw_init()).done(function() {
                         init_deferred.resolve();
                         track.container_div.removeClass("nodata error pending");
                         track.request_draw();
@@ -2688,7 +2687,29 @@ extend(Track.prototype, Drawable.prototype, {
     /**
      * Additional initialization required before drawing track for the first time.
      */
-    predraw_init: function() {},
+    predraw_init: function() {
+        var track = this;
+        return $.getJSON( track.dataset.url(), 
+            {  data_type: 'data', stats: true, chrom: track.view.chrom, low: 0, 
+               high: track.view.max_high, hda_ldda: track.dataset.get('hda_ldda') }, function(result) {
+            track.container_div.addClass( "line-track" );
+            var data = result.data;
+            
+            // Tracks may not have stat data either because there is no data or data is not yet ready.
+            if (data && data.min && data.max) {
+                // Compute default minimum and maximum values
+                var min_value = data.min,
+                    max_value = data.max;
+                // If mean and sd are present, use them to compute a ~95% window
+                // but only if it would shrink the range on one side
+                min_value = Math.floor( Math.min( 0, Math.max( min_value, data.mean - 2 * data.sd ) ) );
+                max_value = Math.ceil( Math.max( 0, Math.min( max_value, data.mean + 2 * data.sd ) ) );
+                // Update the prefs
+                track.prefs.min_value = min_value;
+                track.prefs.max_value = max_value;
+            }
+        });
+    },
 
     /**
      * Returns all drawables in this drawable.
@@ -2800,6 +2821,32 @@ extend(TiledTrack.prototype, Drawable.prototype, Track.prototype, {
         };
     },
 
+    /**
+     * Set track bounds for current chromosome.
+     */
+    set_min_max: function() {
+        var track = this;
+
+        return $.getJSON( track.dataset.url(), 
+            { data_type: 'data', stats: true, chrom: track.view.chrom, low: 0, 
+              high: track.view.max_high, hda_ldda: track.dataset.get('hda_ldda') }, 
+            function(result) {
+                var data = result.data;
+                if ( isNaN(parseFloat(track.prefs.min_value)) || isNaN(parseFloat(track.prefs.max_value)) ) {
+                    // Compute default minimum and maximum values
+                    var min_value = data.min,
+                        max_value = data.max;
+                    // If mean and sd are present, use them to compute a ~95% window
+                    // but only if it would shrink the range on one side
+                    min_value = Math.floor( Math.min( 0, Math.max( min_value, data.mean - 2 * data.sd ) ) );
+                    max_value = Math.ceil( Math.max( 0, Math.min( max_value, data.mean + 2 * data.sd ) ) );
+                    // Update the prefs
+                    track.prefs.min_value = min_value;
+                    track.prefs.max_value = max_value;
+                }
+            });
+    },
+
     /**
      * Change track's mode.
      */
@@ -2808,6 +2855,10 @@ extend(TiledTrack.prototype, Drawable.prototype, Track.prototype, {
         // TODO: is it necessary to store the mode in two places (.mode and track_config)?
         track.mode = new_mode;
         track.config.values['mode'] = new_mode;
+        // FIXME: find a better way to get Auto data w/o clearing cache; using mode in the
+        // data manager would work if Auto data were checked for compatibility when a specific
+        // mode is chosen.
+        if (new_mode === 'Auto') { this.data_manager.clear(); }
         track.request_draw(true);
         this.action_icons.mode_icon.attr("title", "Set display mode (now: " + track.mode + ")");
         return track;
@@ -2954,10 +3005,11 @@ extend(TiledTrack.prototype, Drawable.prototype, Track.prototype, {
     /**
      * Add a maximum/minimum label to track.
      */
-    _add_yaxis_label: function(type, val, pref_name, on_change) {
+    _add_yaxis_label: function(type, on_change) {
         var track = this,
             css_class = (type === 'max' ? 'top' : 'bottom'),
             text = (type === 'max' ? 'max' : 'min'),
+            pref_name = (type === 'max' ? 'max_value' : 'min_value'),
             // Default action for on_change is to redraw track.
             on_change = on_change || function() { 
                 track.request_draw(true); 
@@ -2966,11 +3018,11 @@ extend(TiledTrack.prototype, Drawable.prototype, Track.prototype, {
 
         if (label.length !== 0) {
             // Label already exists, so update value.
-            label.text(val);
+            label.text(track.prefs[pref_name]);
         }
         else {
             // Add label.
-            label = $("<div/>").text(val).make_text_editable({
+            label = $("<div/>").text(track.prefs[pref_name]).make_text_editable({
                 num_cols: 12,
                 on_finish: function(new_val) {
                     $(".bs-tooltip").remove();
@@ -2989,6 +3041,29 @@ extend(TiledTrack.prototype, Drawable.prototype, Track.prototype, {
      * drawn/fetched and shown.
      */
     postdraw_actions: function(tiles, width, w_scale, clear_after) {
+        //
+        // If some tiles have line track tiles (which denote coverage data), redraw all tiles using coverage data.
+        //
+        var non_line_track_tiles = _.filter(tiles, function(tile) {
+            return !(tile instanceof LineTrackTile);
+        });
+
+        if (tiles.length !== non_line_track_tiles.length) {
+            // Clear because this is set when drawing.
+            this.max_height_px = 0;
+            var track = this;
+            _.each(non_line_track_tiles, function(tile) {
+                tile.html_elt.remove();
+                track.draw_helper(true, tile.region, tile.resolution, track.tiles_div, w_scale, { mode: 'Coverage' });
+            });
+
+            track._add_yaxis_label('max');
+        }
+        else {
+           // Remove Y-axis labels because there are no line track tiles.
+           this.container_div.find('.yaxislabel').remove();
+        }
+
         //
         // If some tiles have icons, set padding of tiles without icons so features and rows align.
         //
@@ -3004,16 +3079,6 @@ extend(TiledTrack.prototype, Drawable.prototype, Track.prototype, {
                 }
             });
         }
-
-        //
-        // If using SummaryTree tiles, show max.
-        //
-        var track = this,
-            first_tile = tiles[0];
-        if (first_tile instanceof SummaryTreeTile) {
-            var max_val = (this.prefs.histogram_max ? this.prefs.histogram_max : first_tile.max_val);
-            this._add_yaxis_label('max', max_val, 'histogram_max');
-        }
     },
 
     /**
@@ -3021,12 +3086,13 @@ extend(TiledTrack.prototype, Drawable.prototype, Track.prototype, {
      * jQuery.Deferred object that is fulfilled when tile can be drawn again.
      */ 
     draw_helper: function(force, region, resolution, parent_element, w_scale, kwargs) {
-        var track = this,
-            key = this._gen_tile_cache_key(w_scale, region),
-            is_tile = function(o) { return (o && 'track' in o); };
-            
         // Init kwargs if necessary to avoid having to check if kwargs defined.
         if (!kwargs) { kwargs = {}; }
+
+        var track = this,
+            key = this._gen_tile_cache_key(w_scale, region),
+            is_tile = function(o) { return (o && 'track' in o); },
+            mode = kwargs.mode || track.mode;
                        
         // Check tile cache, if found show existing tile in correct position
         var tile = (force ? undefined : track.tile_cache.get_elt(key));
@@ -3041,7 +3107,7 @@ extend(TiledTrack.prototype, Drawable.prototype, Track.prototype, {
         var can_draw_now = true;
         
         // Get the track data, maybe a deferred
-        var tile_data = track.data_manager.get_data(region, track.mode, resolution, track.data_url_extra_params);
+        var tile_data = track.data_manager.get_data(region, mode, resolution, track.data_url_extra_params);
         if ( is_deferred( tile_data ) ) {
             can_draw_now = false;
         }
@@ -3049,7 +3115,7 @@ extend(TiledTrack.prototype, Drawable.prototype, Track.prototype, {
         // Get reference data if needed, maybe a deferred
         var seq_data;
         if ( view.reference_track ) {
-            seq_data = view.reference_track.data_manager.get_data(region, track.mode, resolution, view.reference_track.data_url_extra_params);
+            seq_data = view.reference_track.data_manager.get_data(region, mode, resolution, view.reference_track.data_url_extra_params);
             if ( is_deferred( seq_data ) ) {
                 can_draw_now = false;
             }
@@ -3066,7 +3132,6 @@ extend(TiledTrack.prototype, Drawable.prototype, Track.prototype, {
             
             // HACK: this is FeatureTrack-specific.
             // If track mode is Auto, determine mode and update.
-            var mode = track.mode;
             if (mode === "Auto" && track.get_mode) {
                 mode = track.get_mode(tile_data);
                 track.update_auto_mode(mode);
@@ -3079,7 +3144,6 @@ extend(TiledTrack.prototype, Drawable.prototype, Track.prototype, {
                 tile_high = region.get('end'),
                 width = Math.ceil( (tile_high - tile_low) * w_scale ) + track.left_offset,
                 height = track.get_canvas_height(tile_data, mode, w_scale, width);
-            
             canvas.width = width;
             canvas.height = height;
             var ctx = canvas.getContext('2d');
@@ -3115,12 +3179,14 @@ extend(TiledTrack.prototype, Drawable.prototype, Track.prototype, {
     },
 
     /**
-     * Draw a track tile for summary tree data.
+     * Draw line (bigwig) data onto tile.
      */
-    _draw_summary_tree_tile: function(result, ctx, region, resolution, w_scale) {
-        var painter = new painters.SummaryTreePainter(result, region.get('start'), region.get('end'), this.prefs);
-        painter.draw(ctx, ctx.canvas.width, ctx.canvas.height, w_scale);
-        return new SummaryTreeTile(this, region, resolution, ctx.canvas, result.data, result.max);
+    _draw_line_track_tile: function(result, ctx, mode, resolution, region, w_scale) {
+        var canvas = ctx.canvas,
+            painter = new painters.LinePainter(result.data, region.get('start'), region.get('end'), this.prefs, mode);
+        painter.draw(ctx, canvas.width, canvas.height, w_scale);
+        
+        return new LineTrackTile(this, region, resolution, canvas, result.data);
     },
 
     /**
@@ -3277,10 +3343,17 @@ var LabelTrack = function (view, container) {
 };
 extend(LabelTrack.prototype, Track.prototype, {
     build_header_div: function() {},
+
     init: function() {
         // Enable by default because there should always be data when drawing track.
         this.enabled = true;  
     },
+
+    /**
+     * Additional initialization required before drawing track for the first time.
+     */
+    predraw_init: function() {},
+
     _draw: function() {
         var view = this.view,
             range = view.high - view.low,
@@ -3623,8 +3696,8 @@ extend(CompositeTrack.prototype, TiledTrack.prototype, {
             t = function() { track.update_all_min_max(); };
 
         // Add min, max labels.
-        this._add_yaxis_label('min', this.drawables[0].prefs.min_value, 'min_value', t);
-        this._add_yaxis_label('max', this.drawables[0].prefs.max_value, 'max_value', t);
+        this._add_yaxis_label('min', t);
+        this._add_yaxis_label('max', t);
     }
 });
 
@@ -3655,6 +3728,11 @@ extend(ReferenceTrack.prototype, Drawable.prototype, TiledTrack.prototype, {
         this.enabled = true;
     },
 
+    /**
+     * Additional initialization required before drawing track for the first time.
+     */
+    predraw_init: function() {},
+
     can_draw: Drawable.prototype.can_draw,
 
     /**
@@ -3716,42 +3794,15 @@ var LineTrack = function (view, container, obj_dict) {
         saved_values: obj_dict.prefs,
         onchange: function() {
             track.set_name(track.prefs.name);
-            track.vertical_range = track.prefs.max_value - track.prefs.min_value;
             track.request_redraw(true);
         }
     });
 
     this.prefs = this.config.values;
     this.visible_height_px = this.config.values.height;
-    this.vertical_range = this.config.values.max_value - this.config.values.min_value;
 };
 extend(LineTrack.prototype, Drawable.prototype, TiledTrack.prototype, {
     
-    predraw_init: function() {
-        var track = this;
-        track.vertical_range = undefined;
-        return $.getJSON( track.dataset.url(), 
-            {  data_type: 'data', stats: true, chrom: track.view.chrom, low: 0, 
-               high: track.view.max_high, hda_ldda: track.dataset.get('hda_ldda') }, function(result) {
-            track.container_div.addClass( "line-track" );
-            var data = result.data;
-            if ( isNaN(parseFloat(track.prefs.min_value)) || isNaN(parseFloat(track.prefs.max_value)) ) {
-                // Compute default minimum and maximum values
-                var min_value = data.min,
-                    max_value = data.max;
-                // If mean and sd are present, use them to compute a ~95% window
-                // but only if it would shrink the range on one side
-                min_value = Math.floor( Math.min( 0, Math.max( min_value, data.mean - 2 * data.sd ) ) );
-                max_value = Math.ceil( Math.max( 0, Math.min( max_value, data.mean + 2 * data.sd ) ) );
-                // Update the prefs
-                track.prefs.min_value = min_value;
-                track.prefs.max_value = max_value;
-            }
-            track.vertical_range = track.prefs.max_value - track.prefs.min_value;
-            track.total_frequency = data.total_frequency;
-        });
-    },
-
     /**
      * Actions to be taken before drawing.
      */
@@ -3759,18 +3810,10 @@ extend(LineTrack.prototype, Drawable.prototype, TiledTrack.prototype, {
     before_draw: function() {},
 
     /**
-     * Draw LineTrack tile.
+     * Draw track tile.
      */
     draw_tile: function(result, ctx, mode, resolution, region, w_scale) {
-        // Paint onto canvas.
-        var 
-            canvas = ctx.canvas,
-            tile_low = region.get('start'),
-            tile_high = region.get('end'),
-            painter = new painters.LinePainter(result.data, tile_low, tile_high, this.prefs, mode);
-        painter.draw(ctx, canvas.width, canvas.height, w_scale);
-        
-        return new Tile(this, region, resolution, canvas, result.data);
+        return this._draw_line_track_tile(result, ctx, mode, resolution, region, w_scale);
     },
 
     /**
@@ -3811,14 +3854,12 @@ var DiagonalHeatmapTrack = function (view, container, obj_dict) {
         saved_values: obj_dict.prefs,
         onchange: function() {
             track.set_name(track.prefs.name);
-            track.vertical_range = track.prefs.max_value - track.prefs.min_value;
             this.request_redraw(true);
         }
     });
 
     this.prefs = this.config.values;
     this.visible_height_px = this.config.values.height;
-    this.vertical_range = this.config.values.max_value - this.config.values.min_value;
 };
 extend(DiagonalHeatmapTrack.prototype, Drawable.prototype, TiledTrack.prototype, {
     /**
@@ -3863,7 +3904,8 @@ var FeatureTrack = function(view, container, obj_dict) {
             { key: 'label_color', label: 'Label color', type: 'color', default_value: 'black' },
             { key: 'show_counts', label: 'Show summary counts', type: 'bool', default_value: true, 
               help: 'Show the number of items in each bin when drawing summary histogram' },
-            { key: 'histogram_max', label: 'Histogram maximum', type: 'float', default_value: null, help: 'clear value to set automatically' },
+            { key: 'min_value', label: 'Histogram minimum', type: 'float', default_value: null, help: 'clear value to set automatically' },
+            { key: 'max_value', label: 'Histogram maximum', type: 'float', default_value: null, help: 'clear value to set automatically' },
             { key: 'connector_style', label: 'Connector style', type: 'select', default_value: 'fishbones',
                 options: [ { label: 'Line with arrows', value: 'fishbone' }, { label: 'Arcs', value: 'arcs' } ] },
             { key: 'mode', type: 'string', default_value: this.mode, hidden: true },
@@ -3905,12 +3947,14 @@ extend(FeatureTrack.prototype, Drawable.prototype, TiledTrack.prototype, {
      * drawn/fetched and shown.
      */
     postdraw_actions: function(tiles, width, w_scale, clear_after) {
-        TiledTrack.prototype.postdraw_actions.call(this, tiles, clear_after);
+        TiledTrack.prototype.postdraw_actions.call(this, tiles, width, w_scale, clear_after);
         
         var track = this,
             i;
                 
         // If mode is Coverage and tiles do not share max, redraw tiles as necessary using new max.
+        /*
+        This code isn't used right now because Coverage mode uses predefined max in preferences.
         if (track.mode === "Coverage") {
             // Get global max.
             var global_max = -1;
@@ -3928,7 +3972,8 @@ extend(FeatureTrack.prototype, Drawable.prototype, TiledTrack.prototype, {
                     track.draw_helper(true, tile.index, tile.resolution, tile.html_elt.parent(), w_scale, { more_tile_data: { max: global_max } } );
                 }
             }
-        }            
+        }
+        */           
         
         //
         // Update filter attributes, UI.
@@ -3992,17 +4037,17 @@ extend(FeatureTrack.prototype, Drawable.prototype, TiledTrack.prototype, {
             this.action_icons.show_more_rows_icon.hide();
         }
     },
+
     update_auto_mode: function( mode ) {
         var mode;
         if ( this.mode === "Auto" ) {
             if ( mode === "no_detail" ) {
                 mode = "feature spans";
-            } else if ( mode === "summary_tree" ) {
-                mode = "coverage histogram";
             }
             this.action_icons.mode_icon.attr("title", "Set display mode (now: Auto/" + mode + ")");
         }
     },
+
     /**
      * Place features in slots for drawing (i.e. pack features).
      * this.slotters[level] is created in this method. this.slotters[level]
@@ -4022,15 +4067,13 @@ extend(FeatureTrack.prototype, Drawable.prototype, TiledTrack.prototype, {
 
         return slotter.slot_features( features );
     },
+
     /**
      * Returns appropriate display mode based on data.
      */
     get_mode: function(data) {
-        if (data.dataset_type === "summary_tree") {
-            mode = "summary_tree";
-        } 
         // HACK: use no_detail mode track is in overview to prevent overview from being too large.
-        else if (data.extra_info === "no_detail" || this.is_overview) {
+        if (data.extra_info === "no_detail" || this.is_overview) {
             mode = "no_detail";
         } 
         else {
@@ -4054,12 +4097,13 @@ extend(FeatureTrack.prototype, Drawable.prototype, TiledTrack.prototype, {
         }
         return mode;
     },
+
     /**
      * Returns canvas height needed to display data; return value is an integer that denotes the
      * number of pixels required.
      */
     get_canvas_height: function(result, mode, w_scale, canvas_width) {
-        if (mode === "summary_tree" || mode === "Coverage") {
+        if (mode === "Coverage" || result.dataset_type === 'bigwig') {
             return this.summary_draw_height;
         }
         else {
@@ -4071,6 +4115,7 @@ extend(FeatureTrack.prototype, Drawable.prototype, TiledTrack.prototype, {
             return Math.max(MIN_TRACK_HEIGHT, dummy_painter.get_required_height(rows_required, canvas_width) );
         }
     },
+
     /**
      * Draw FeatureTrack tile.
      * @param result result from server
@@ -4087,10 +4132,10 @@ extend(FeatureTrack.prototype, Drawable.prototype, TiledTrack.prototype, {
             tile_low = region.get('start'),
             tile_high = region.get('end'),
             left_offset = this.left_offset;
-        
-        // Drawing the summary tree.
-        if (mode === "summary_tree" || mode === "Coverage") {
-            return this._draw_summary_tree_tile(result, ctx, region, resolution, w_scale);
+
+        // If data is line track data, draw line track tile.
+        if (result.dataset_type === 'bigwig') {
+            return this._draw_line_track_tile(result, ctx, 'Histogram', resolution, region, w_scale);
         }
 
         // Handle row-by-row tracks
@@ -4147,6 +4192,7 @@ extend(FeatureTrack.prototype, Drawable.prototype, TiledTrack.prototype, {
         
         return new FeatureTrackTile(track, region, resolution, canvas, result.data, w_scale, mode, result.message, all_slotted, feature_mapper);        
     },
+
     /**
      * Returns true if data is compatible with a given mode.
      */
@@ -4155,24 +4201,25 @@ extend(FeatureTrack.prototype, Drawable.prototype, TiledTrack.prototype, {
         if (mode === "Auto") {
             return true;
         }
-        // Histogram mode requires summary_tree data.
+        // Histogram mode requires bigwig data.
         else if (mode === "Coverage") {
-            return data.dataset_type === "summary_tree";
+            return data.dataset_type === "bigwig";
         }
         // All other modes--Dense, Squish, Pack--require data + details.
-        else if (data.extra_info === "no_detail" || data.dataset_type === "summary_tree") {
+        else if (data.extra_info === "no_detail") {
             return false;
         }
         else {
             return true;
         }
     },
+
     /**
      * Returns true if data can be subsetted.
      */
     can_subset: function(data) {
-        // Do not subset summary tree data, entries with a message, or data with no detail.
-        if (data.dataset_type === "summary_tree" || data.message || data.extra_info === "no_detail")  {
+        // Do not subset entries with a message or data with no detail.
+        if (data.dataset_type === 'bigwig' || data.message || data.extra_info === "no_detail")  {
             return false;
         }
 
@@ -4217,9 +4264,9 @@ extend(VariantTrack.prototype, Drawable.prototype, TiledTrack.prototype, {
      * Draw tile.
      */
     draw_tile: function(result, ctx, mode, resolution, region, w_scale) {
-        // Data could be summary tree data or variant data.
-        if (result.dataset_type === 'summary_tree') {
-            return this._draw_summary_tree_tile(result, ctx, region, resolution, w_scale);
+        // Data could be coverage data or variant data.
+        if (result.dataset_type === 'bigwig') {
+            return this._draw_line_track_tile(result, ctx, "Histogram", region, resolution, w_scale);
         }
         else { // result.dataset_type === 'variant'
             var view = this.view,
@@ -4235,7 +4282,7 @@ extend(VariantTrack.prototype, Drawable.prototype, TiledTrack.prototype, {
      * number of pixels required.
      */
     get_canvas_height: function(result, mode, w_scale, canvas_width) {
-        if (result.dataset_type === 'summary_tree') {
+        if (result.dataset_type === 'bigwig') {
             return this.summary_draw_height;
         }
         else {
@@ -4264,9 +4311,11 @@ extend(VariantTrack.prototype, Drawable.prototype, TiledTrack.prototype, {
      * Additional initialization required before drawing track for the first time.
      */
     predraw_init: function() {
+        var deferreds = [ Track.prototype.predraw_init.call(this) ];
         if (!this.dataset.get_metadata('sample_names')) {
-            return this.dataset.fetch();
+            deferreds.push(this.dataset.fetch());
         }
+        return deferreds;
     },
 
     /**
@@ -4277,7 +4326,7 @@ extend(VariantTrack.prototype, Drawable.prototype, TiledTrack.prototype, {
         TiledTrack.prototype.postdraw_actions.call(this, tiles, width, w_scale, clear_after);
 
         // Add summary/sample labels if needed and not already included.
-        if ( !(tiles[0] instanceof SummaryTreeTile) && this.prefs.show_labels) {
+        if ( !(tiles[0] instanceof LineTrackTile) && this.prefs.show_labels) {
             var font_size;
 
             // Add and/or style labels.
@@ -4343,7 +4392,6 @@ var ReadTrack = function (view, container, obj_dict) {
             { key: 'show_insertions', label: 'Show insertions', type: 'bool', default_value: false },
             { key: 'show_differences', label: 'Show differences only', type: 'bool', default_value: true },
             { key: 'show_counts', label: 'Show summary counts', type: 'bool', default_value: true },
-            { key: 'histogram_max', label: 'Histogram maximum', type: 'float', default_value: null, help: 'Clear value to set automatically' },
             { key: 'mode', type: 'string', default_value: this.mode, hidden: true }
         ], 
         saved_values: obj_dict.prefs,
diff --git a/static/scripts/viz/visualization.js b/static/scripts/viz/visualization.js
index c80ccc68e85..ada037dcf75 100644
--- a/static/scripts/viz/visualization.js
+++ b/static/scripts/viz/visualization.js
@@ -505,9 +505,6 @@ var GenomeDataManager = Cache.extend({
             // FIXME: constant should go somewhere.
             extra_params.num_samples = 1000 * detail_multiplier;
         }
-        else if (cur_data.dataset_type === 'summary_tree') {
-            extra_params.level = Math.min(cur_data.level - 1, 2);
-        }
 
         return this.load_data(region, mode, resolution, extra_params);
     },
@@ -579,7 +576,7 @@ var GenomeDataManager = Cache.extend({
                            data_point[0] <= subregion.get('end');
                 });
             },
-            'refseq': function(data, subregion) {
+            refseq: function(data, subregion) {
                 var seq_start = subregion.get('start') - entry.region.get('start'),
                     seq_end = entry.data.length - ( entry.region.get('end') - subregion.get('end') );
                 return entry.data.slice(seq_start, seq_end);