These generic filter controls should work by "where clause" and should be allowed on any item based track including bigBeds! Note that bigBeds already support scoreFilter and will always have the problem that zoomed out will not support filtering. The Browser UI should show when tracks are filtered, so that losing the filter is obvious!

filter.<fieldName> <default integer>
filterByRange.<fieldName> <off/on>
filterLimits.<fieldName> <low>[:<high>]

There are a number of different filters available for bigBed data. See the Filters Quick Start guide for more info. Note: for configurable features, like filters, an additional period "." or plus "+" is required in the type declaration, for instance type bigBed 5 . or type bigBed 9 +.

VCF tracks: the settings filter.*, filterByRange.*, - filterLimits.*, filterText.*, filterValues.*, - filterValuesDefault.*, filterType.*, filterLabel.* - and filterPriority.* also work on vcfTabix and vcf - tracks. There, <fieldName> is the key of an INFO field, e.g. - filter.AF 0.01 or filterText.CSQ *missense*. - The key must be declared in an ##INFO line of the VCF header; the - header's Description is the default label of the filter. In addition, the - fixed columns ID and QUAL can be used as field names. These - filters are combined with the other VCF filters (minimum QUAL, FILTER column, minimum - allele frequency and count). The details for VCF values:

If a field has more than one value, e.g. Number=A with one value per - alternate allele, the variant passes if any one of its values passes. With - filterType multipleListOr or multipleListAnd, the values are - compared as a list, like a comma-separated bigBed field.
A missing value (.), or a variant without this INFO key, never passes a - numeric filter. For text and value filters, it is compared as an empty string, so the - default wildcard * still shows it.
A Flag field has the value 1 if the key is present and 0 if not, so - filter.DB 1 shows only variants with the flag, and - filterValues.DB 1|present,0|absent makes a menu.

Example:

-    track myVariants
-    type vcfTabix
-    filter.AF 0.01
-    filterByRange.AC on
-    filter.AC 2:100
-    filterLimits.AC 0:1000
-    filterText.CSQ *
-    filterLabel.CSQ Consequence

filter.<fieldName> is used for numerical data. It requires a default value to be passed. A value of 0 (or the lowest value present in the dataset) can be used to enable numerical filtering, but filter nothing by default.

By default, the range of values for filter.<fieldName> is 0 to 1000. However, you can explicitly set the upper and lower limits of the filter with filterLimits.<fieldName>.

The numeric filters will exclude items that fall below the setting. That is, a filter.<fieldName> of 800 will exclude all items with a score below 800. You can also filter values within a range by including the filterByRange.<fieldName> setting. For example, filter.<fieldName> 800:900 will include only items with scores at or above 800 and below 900. It is recommended that filterByRange.<fieldName> be used in combination with filterLimits.<fieldName> to set limit boundaries.

The filter label will be the description of the field as specified by the autoSql (.as) file. @@ -1892,31 +1859,31 @@ 5 6 (Uncertain) Unknown 7.0

This example applies filter.<fieldName> to values in the field named confidenceScore containing some non-numerical values. If items with the four values above were filtered with a minimum value of 6:

5 - item would be removed as it is less than the filter value
6 (Uncertain) - item should show up, as it would be interpreted as "6"
Unknown - item would be removed as it would be interpreted as 0
7.0 - item would appear as decimals are supported

filterText.<fieldName> <default search string>
filterType.<fieldName> <wildcard/regexp>

filterText.<fieldName> is used to enable text searching in the specified fieldName. It requires a default search string to be passed. An asterisk/wildcard (*) can be used to enable text searching, but pass no default value. If a word or string is passed, items matching the string will be filtered by default. See examples below for details.

filterText.<fieldName> will enable two kinds of searching, wildcard and @@ -1958,31 +1925,31 @@ filterText.geneName *

This example is enabling filtering on the same field as above, geneName, however, it is not declaring a default search parameter. This is done by passing only an asterisk/wildcard (*). This means that the search box will be present but no geneName items will be filtered out of the data unless the user specifies a value.

     filterText.geneName \.1$
     filterType.geneName regexp

This example once again enables filtering on the same field, however, it is declaring regexp as the filter type and passing a regular expression to be applied by default. In this case, we are targeting all geneName items that are version 1.

filterValues.<fieldName> <value1,value2,value3...>
filterValuesDefault.<fieldName> <value1,value2,value3...>

filterType.<fieldName> <single/singleList/multiple/multipleListOr/multipleListAnd/multipleListOnlyOr/multipleListOnlyAnd>

filterValues.<fieldName> is used to enable filtering by specified values within a field. It can be used on fields that can contain one text value or a list of comma-separated values of text, like "classA,classB". Usually these are category names. The option requires at least one value to filter on.

@@ -2078,51 +2045,51 @@

     filterValues.annotationType DNA-BR,AS,BS,BSi

In this example the filter is being applied to multiple values in the annotationType field. We can then select from these values in the annotationType field with a drop-down menu displayed on the track settings page, and display only items that match our selections. The selection choices will let us match one, all, or any combination of the supplied values.

     filterValues.annotationType DNA-BR|DNA-binding region,AS|active site,BS|beta strand,BSi|binding site

In this follow up to the previous question, we have changed the name of the items that show up in the drop down menu to be more descriptive than the dense file format values. This means that if we wanted to only see items with annotationType of DNA-BR, we would select DNA-binding region from the interface menu.