Version 1.3.1 release. Updated source for Exac tolerance dataset (as …

…the original link is now broken).

CHANGELOG.md

@@ -1,6 +1,9 @@
 # Release History
 
-## Version 1.3 (January 8, 2015)
+## Version 1.3.1 (February 1, 2015)
+- Updated source for Exac Tolerance dataset (original link is now broken).
+
+## Version 1.3 (January 25, 2015)
 ## Highlights
 - STMP can now be run in a "test mode" to ensure it is set up correctly. Simply run `python stmp.py --test` to activate this mode. Output will be stored in `(stmp_dir)/data/test/output_unverified` by default, or can be stored in a different directory with the `--output_dir` parameter. If desired, you can compare it against our output (`output_verified`) to see if it is the same (e.g. `diff -rq (stmp_dir)/data/test/output_unverified/ (stmp_dir)/data/test/output_verified/`).
 - STMP now includes SnpEFF annotations as part of the joined annotated output file (previously they were only output as a separate file). Note that the SnpEFF annotated column contains the entire VCF INFO column with added SnpEFF annotation tags.

code/config/datasets.yml

@@ -138,13 +138,13 @@ exac:
 exac_tol:
   Import_If_Missing: True
   License:
-  Source: ftp://ftp.broadinstitute.org/pub/ExAC_release/release0.3/functional_gene_constraint/forweb_cleaned_exac_r03_march16_z_data_pLI.txt
+  Source: ftp://ftp.broadinstitute.org/pub/ExAC_release/release0.3/functional_gene_constraint/fordist_cleaned_exac_r03_march16_z_pli_rec_null_data.txt
   Annotation: exac_tolerance
   Category: region
   StartingLine: 1 # first line (0) is header without #
   Class: tolerance
   Citation:
-  Description: 'ftp://ftp.broadinstitute.org/pub/ExAC_release/release0.3/functional_gene_constraint/README_forweb_cleaned_exac_r03_2015_03_16_z_data_pLI_2015_10_11.txt'
+  Description: 'ftp://ftp.broadinstitute.org/pub/ExAC_release/release0.3/functional_gene_constraint/README_fordist_cleaned_exac_r03_z_data_pLI_2016_01_13.txt'
   ColumnHeaders: [transcript, gene, chr, n_exons, start, end, bp, '', '', '', '', '', '', '', '', '', syn_z, mis_z, lof_z, pLI]
   DataType: ['varchar(2)', 'int', 'varchar(25)', 'int', 'int', 'int', 'int', '', '', '', '', '', '', '', '', '', 'float', 'float', 'float', 'float']