Batch rsID Bugfix

Bugfixes:

• Due to eLink incompatibility with ePost, the vcf and rsID were not correctly fetching more than 1000 variants, which has now been fixed. Slight loss of performance due to the modified information lookup. Will look to speed things up in the future.

Updates:

• there is a new --long-log file option that logs all debugs and above. The current --log option only logs warnings and above to reduce file size.
• log files now use the outprefix name instead of 'clinotator.log'

Bugfixes and decimal math

Updates:

• python 2 compatibility fix, runs on 2.7 now, added exception time.time option if no time.perf_counter.
• added Decimal math for better consistency in CTRS calculation.

Bugfixes:

• corrected bin edges for CTPS, negative values include right edge, positive values include left edge.
• modified logging for more info.
• no CTRS score calculated below 2 assertions.

Calibration of CTWS and CTRR

Update:

• The CWTS and resulting CTRR scales have been calibrated with >99% prediction intervals for each clinical sigificance.

Bugfixes:

• missing rsid and minor allele fields are filled in with "."

Reclassification Recommendations Reworked

Bugfixes:

• CTRR and CTWS no longer provided for less than 2 clinical assertions

Updates:

• Implementation of Reclassification Recommendations and retooling the Weighted Significance.

Minor bugfixes and global variables file

Bugfixes:

• Filter empty lines from the input files to fix http error from querying empty list items.

• Replace ";" and "," in vcf output file fields to capitalized percent encoding as directed in VCF v4.3 specifications. Also stops unneccesary quotation of INFO field.

Update:

• Moved global variables to global_vars.py file for easier configuration.

VCF Parsing Implemented

• The vcf option is now functional. It will parse vcf by rsid, return a table and generate an annotated version of the vcf.

• The outfile prefix option "-o" has been Modified.

• A log file option has been incorporated.

• Numpy RuntimeWarning reporting has been fixed to correctly warn to stdin or log file.

Initial pre-release version

This version contains the initial rsid and vid inputs, and the uncalibrated raw scoring metrics. Vcf processing currently under construction.