How to install and set up a local UCSC BLAT environment

Downloading BLAT To get BLAT source code: Patching (optional) I decided to make blat a static binary to avoid missing shared library errors. Here’s a patch you can use to modify the blat makefile: You may need static library packages installed on your system. The names of these packages will depend on your version […]

Speedy BED conversion tool: convert2bed

Finishing touches are in place for my convert2bed tool (GitHub site). This utility converts common genomics data formats (BAM, GFF, GTF, PSL, SAM, VCF, WIG) to lexicographically-sorted UCSC BED format. It offers two benefits over alternatives: It runs about 3-10x as fast as bedtools *ToBed equivalents It converts all input fields in as non-lossy a […]

Regression testing of SHA-1 signatures via command-line

I wrote a data extraction utility which uses PolarSSL to export a Base64-encoded SHA-1 digest of some internal metadata (a string of JSON-formatted data), to help validate archive integrity: $ unstarch –sha1-signature .foo 7HkOxDUBJd2rU/CQ/zigR84MPTc= So far, so good. But now I want to validate that the metadata are being digested correctly through some independent means, […]