1e5471fab322302a10e19adf907ff26e020535f0
max
  Thu Jun 22 12:55:37 2023 +0200
adding -bed option to bigBedToBed, also removing the -maxItems option as it never worked, is not used anywhere at least in our code repo and also fixing the documentation page and a typo in the usage docs and the documentation page. refs #31531

diff --git src/hg/htdocs/goldenPath/help/cloud.html src/hg/htdocs/goldenPath/help/cloud.html
index 08832d3..a73904f 100755
--- src/hg/htdocs/goldenPath/help/cloud.html
+++ src/hg/htdocs/goldenPath/help/cloud.html
@@ -369,32 +369,32 @@
 <h2>How do I extract data from the bigBed/2bit data formats?</h2>
 <p>
 A lot of our data is stored in a binary indexed version called bigBed. This format
 saves space and also allows the extraction of information based on the first three fields
 (chrom, chromStart, chromEnd), which define annotation coordinate location.</p>
 <p>
 To pull information out of bigBed files there is a tool called <code>bigBedToBed</code>.
 By running the command by itself you can see the command options. 
 <pre>
 bigBedToBed v1 - Convert from bigBed to ascii bed format.
 usage:
    bigBedToBed input.bb output.bed
 options:
    -chrom=chr1 - if set restrict output to given chromosome
    -start=N - if set, restrict output to only that over start
-   -end=N - if set, restict output to only that under end
-   -maxItems=N - if set, restrict output to first N items
+   -end=N - if set, restrict output to only that under end
+   -bed=in.bed - restrict output to all regions in a BED file
    -udcDir=/dir/to/cache - place to put cache for remote bigBed/bigWigs
    -header - output a autoSql-style header (starts with '#').
 </pre></p>
 <p>
 Another similar tool is available to extract data from the binary indexed 2bit sequence
 storage format. The tool <code>twoBitToFa</code> can be given coordinate ranges and the
 DNA can be extracted from the file.</p>
 <h3>Examples</h3>
 <p>
 <ul>
 <li>For instance, here is an example of accessing the hg38 2bit human assembly sequence file
 hosted at the s3 Amazon bucket and extracting a small coordinate range:
 <pre>
 twoBitToFa -seq=chr1 -start=1234500 -end=1234600 http://genome-browser.s3-website-us-east-1.amazonaws.com/gbdb/hg38/hg38.2bit stdout
 >chr1:1234500-1234600