US 9,811,439 B1
Functional testing of code modifications for read processing systems
Ryan Barrett, San Francisco, CA (US); and Krishna Pant, San Jose, CA (US)
Assigned to COLOR GENOMICS, INC., Burlingame, CA (US)
Filed by Ryan Barrett, San Francisco, CA (US); and Krishna Pant, San Jose, CA (US)
Filed on Apr. 17, 2017, as Appl. No. 15/489,492.
Claims priority of provisional application 62/324,078, filed on Apr. 18, 2016.
Int. Cl. G06F 9/44 (2006.01); G06F 11/36 (2006.01); G06F 11/26 (2006.01)
CPC G06F 11/3612 (2013.01) [G06F 11/26 (2013.01)] 20 Claims
OG exemplary drawing
 
1. A method for using functional testing to detect run-time impacts of code modifications, the method comprising:
accessing a workflow for processing reads, the workflow including a plurality of stages, at least one stage of the plurality of stages being performed via execution of a modifiable code, the plurality of stages including:
a first stage for aligning each of a plurality of reads with a corresponding portion of a reference data set, the first stage being defined based on first modifiable code, the reference data set including a reference sequence; and
a second stage for collectively analyzing data corresponding to the aligned reads, the second stage being defined based on second modifiable code;
identifying functional testing specifications to correspond with the workflow, wherein the functional testing specifications include:
a definition of at least part of the workflow to be conducted during functional testing, the at least part of the workflow including one or more stages of the plurality of stages;
a reduced reference data set to be used in place of the reference data set in the functional testing, a size of the reduced reference data set being smaller than a size of the reference data set; and
read data that includes a set of reads to be used as input for the functional testing, each read of the set of reads including a sequence that identifies set of bases, the set of bases being arranged in a particular order in the read;
performing the functional testing for the at least part of the workflow, the functional testing including performing the one or more stages of the workflow using the read data and the reduced reference data set, wherein performing the one or more stages of the workflow includes performing a modified version of at least one modifiable code of a plurality of modifiable codes, the plurality of modifiable codes including the first modifiable code and the second modifiable code, and each of the plurality of modifiable codes corresponding to a stage of the plurality of stages of the workflow;
detecting a result generated via the performance of the functional testing for the at least part of the workflow;
outputting the result;
determining that the workflow is to be updated; and
in response to determining that the workflow is to be updated, updating a version of the workflow to include the modified version of the at least one modifiable code.