Bioinformatics Tools Series

This continues the series of posts meant to help you write concise and well-tested bioinformatic tools. We previously wrote a tool to ensure that the NM/UQ/MD SAM tags on each read are accurate.  Lets add some logging information to the tool, to print out the input and output SAM or BAM file paths, and report some progress … Read More

This continues the series of posts meant to help you write concise and well-tested bioinformatic tools. Lets write a tool that reads a BAM file, does some modification to the records, then writes a BAM file. Lets ensure that the NM/UQ/MD SAM tags on each read are accurate, which is important if aligners aren’t well-behaved … Read More

This continues the series of posts meant to help you write concise and well-tested bioinformatic tools. One common thing to do is to retrieve, set, or update the SAM optional tags on each SAM record.  The SAM optional fields (tags) specification lists predefined standard tags, though users can add their own (start with a X, Y, … Read More

This is the start of a series of posts introducing various ways of implementing cohesive, concise, and well-tested bioinformatic tools in scala using many of the APIs found in fgbio (see the latest scaladoc, list of tools, and list of metrics).  Each post will be build on each other to help familiarize folks with how I build simple … Read More