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changes.txt
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August 12, 2024
added map to qtlMapper for db_snp source with newly added db_snp data for human 37
July 2024
updating qtlMapper for GWAS and improve dbSNP get method
Jun 26, 2024
updated dependencies
February 21, 2024
qtl mapper: updating to create map data for new GWAS qtls
Sep 12, 2023
strain mapper: logic fixes
Sep 11, 2023
strain mapper: mutant strains having allelic variants derive their positions from positions of those allelic variants
Sep 01, 2023
Feb 22, 2023
updated dependencies
Feb 06, 2023
updated build.gradle to be gradle 6.x + compatible
Apr 12, 2022
renamed 'master' to 'main'
Feb 15, 2022
tuned up logging
Feb 15, 2022
renamed distro to 'object-mapper-pipeline'
Feb 11, 2022
updated dbcp to major version 2
Jan 19, 2022
updated log4j to avoid zero day exploit
Apr 27, 2021
mappers: updated to handle rat assembly 7.2
Jul 24, 2020
marker mapper: improved logging
May 28, 2020
updated jar dependencies to fix problem with sql queries
May 10, 2020
updated jar dependencies
Nov 11, 2019
improved logging
Oct 03, 2019
renamed sslpMapper to markerMapper
Jan 17, 2019 -- ver 2.0.4
refactored build.gradle; improved logging
Sep 17, 2018 -- ver 2.0.3
moved from subversion to github
Feb 19, 2018 -- ver 2.0.2
upgraded code to java 8; streamlined logging
Jan 27, 2017 -- ver 2.0.1
QTLMapper: separated generation of out-of-region genes to standalone script
Dec 21, 2016 -- ver 2.0
updated to use GRADLE instead of ANT
Sep 20, 2016 -- ver 1.2.12
StrainMapper: extended mapping of mutant strains to strain types 'mutant_knockin','mutant_knockout'
Jan 27, 2016 -- ver 1.2.11
SslpMapper: tuned up logging
Jan 27, 2016 -- ver 1.2.10
SslpMapper: new mapper for DB_SNP rat SSLPs
QtlMapper: simplified code
StrainMapper: simplified code
May 21, 2015 -- ver 1.2.9
QtlMapper: improved reporting of unpositionable qtls, esp. for mouse
Apr 27, 2015 -- ver 1.2.8
Strain Mapper v.1.2.1: allows positioning of mutant strains
Apr 24, 2015 -- ver 1.2.7
Strain Mapper v.1.2.0: allows handling of multiple regions (for double/triple congenic strains)
Dec 08, 2014 -- ver 1.2.6
QTL + Strain Mapper: uses the exact chromosome sizes for the purpose of positioning strains and qtls
(previously the chromosome size was estimated as the largest stop_pos of genes on the given chromosome)
Sep 24, 2014 -- ver 1.2.5
QTL + Strain Mapper: changed src pipeline to 'RGD_MAPPER_PIPELINE' per communication with Rajni and Jennifer
Sep 5, 2014 -- ver 1.2.4
QTL + Strain Mapper: added support for Rnor_6.0
Feb 4, 2014 -- ver 1.2.3
QTL Mapper v. 1.2:
- improved QC (for flanking markers with START_POS=0, STOP_POS=0 positions)
- improved logging (not relevant information is no longer logged, to improve log readability)
Aug 2, 2013 -- ver 1.2.2
QTL Mapper v. 1.1:
- qtl position changes logged to separate file position_changes.log
and then emailed to interested parties;
- qtls could be positioned on consensus chromosome: if there are multiple markers having positions
on multiple chromosomes, the chromosome that is most frequent is chosen as consensus chromosome
and marker positions on this consensus chr are used to position the qtl
Jan 22, 2013 -- ver 1.2.1
Fixed the confusing messages when processing qtls with obsolete positions.
Dec 7, 2012 -- ver 1.2
Migrated QtlMapper from ftpFileExtracts; QTL mapper is setup to update data also for new assemblies for mouse and rat
Nov 20, 2012 -- ver 1.1
StrainMapper module extended to compute strain positions on rat assembly maps 5.0 (map_key=70)