Diljot Grewal d07e2d53a15 Copy commit hash minor: removed pickle file 18 Dec 2018 Diljot Grewal 6f4db528d94 Copy commit hash added install instructions 18 Dec 2018 Diljot Grewal a29e91c6669 Copy commit hash minor: some stuff in setup was commented out 18 Dec 2018 Diljot Grewal d9f2d9ba53f Copy commit hash fixes: added museq_het command for titan mode 08 Nov 2018 Diljot Grewal 303cfd0f7e1 Copy commit hash fix: added missing filter to header 23 Oct 2018 Diljot Grewal ce450553831 Copy commit hash feature: updated museq vcf format 25 Sep 2018 Diljot Grewal 7d159e59ccb Copy commit hash impr: single setup step for make and retrain models, also adds museq to executables 27 Aug 2018 Diljot Grewal d38e0d7b513 Copy commit hash removing unneeded files 27 Aug 2018 Diljot Grewal 7db374616c4 Copy commit hash minor fix 18 Jul 2017 Diljot Grewal 4fb2e857a31 Copy commit hash skipped positions where only one position in the amplicon passes filtering threshold 18 Jul 2017 Diljot Grewal 3ec71c867e2 Copy commit hash added models trained with anaconda and sklearn 0.13.1 30 Sep 2016 Diljot Grewal 2a993546f07 Copy commit hash removed symlinks from unit test dir 22 Jul 2016 Diljot Grewal 8f5d3d0faa7 Copy commit hash updated pip required 22 Jul 2016 Diljot Grewal 82f4e7cae8f Copy commit hash updated tests: removed tests that checked rmdups setting (since it soesn't exist anymore)
added the new param to the args object 01 Apr 2016 Diljot Grewal 415a16449ee Copy commit hash renamed keep_duplicate_reads to count_duplicate_reads (make more sense now) 01 Apr 2016 Diljot Grewal 5a9b011ad66 Copy commit hash minor fix 31 Mar 2016 Diljot Grewal 2ca569cfac9 Copy commit hash minor fixes 22 Mar 2016 Diljot Grewal 5de22351fcc Copy commit hash updated version 22 Mar 2016 Diljot Grewal 52cc87d85a9 Copy commit hash added an option to turn duplicate read removal on/off 22 Mar 2016 Diljot Grewal 23ceeb90e69 Copy commit hash fixed a bug where lookups for the positions in the manifest tree weren't working as intended. 03 Mar 2016 Diljot Grewal a46a54516e2 Copy commit hash minor updates to metadata 18 Feb 2016 Diljot Grewal 9276f9c3e7f Copy commit hash minor bug fix. 07 Dec 2015 Diljot Grewal 5a54127d357 Copy commit hash MUT-372: added description of INDL filter field to header 23 Nov 2015 MUT-372 Diljot Grewal a630af4edea Copy commit hash updated PL type to integer. 19 Nov 2015 Diljot Grewal a3f1c6f41e2 Copy commit hash fixed a bug where the position calculation wasn't working properly in deep mode. MUT-370 18 Nov 2015 MUT-370 Diljot Grewal a9c74e3c089 Copy commit hash updated version string 06 Nov 2015 Diljot Grewal bd7e4a9f50f Copy commit hash removed unnecessary files. updated preprocessutils to use paired bam reads instead of 2 single bam reads 06 Nov 2015 Diljot Grewal 2f9023a3e30 Copy commit hash added check in parse_manifest (throws error if amnplicon start >= end) 25 Aug 2015 Diljot Grewal 64f8f8232ff Copy commit hash version string updated 09 Jul 2015 Diljot Grewal 000bd76f3cc Copy commit hash MUT-360: make clean removes the build dir 08 Jul 2015 MUT-360 Diljot Grewal fd8c5c92a07 Copy commit hash MUT-361 : return empty list when there are no overlaps between positions and intervals instead of running it on the full chromosome 08 Jul 2015 MUT-361 Diljot Grewal 23b0413c25f Copy commit hash MUT-356: HomoForward function looks at the positions after the original position but the loop could continue after the end of chromosome. Added a check to break if the pos is outside limits. 09 Apr 2015 MUT-356 Diljot Grewal d6a454072b9 Copy commit hash bug fix (the flush function call in export features was calling the private flush which was changed to protected in the previous updates). 01 Apr 2015 Diljot Grewal 7421f925b02 Copy commit hash updated the makefile (takes python and boostpath at commandline) 31 Mar 2015 Diljot Grewal a5914d08adf Copy commit hash updated version 31 Mar 2015 Diljot Grewal 410078d4ab9 Copy commit hash minor formatting updates. 31 Mar 2015 Diljot Grewal f7db19f2bee Copy commit hash updated the INDL flag implementation (takes ratio of all reads with an indel instead of just the variant reads) 30 Mar 2015 Diljot Grewal 414d86bd16f Copy commit hash museq now adds chr if the reference has chr 20 Mar 2015 Diljot Grewal 5081b5e265d Copy commit hash updated tests (failed if order in lists was different) 20 Mar 2015 Diljot Grewal db0ab4ca023 Copy commit hash updated unit tests 20 Mar 2015 Diljot Grewal 72f40176f72 Copy commit hash updated the code to use intervaltree package instead of PyIntervalTree(Deprecated). Refactored preprocessing mode. 20 Mar 2015 Diljot Grewal 9bda5c3c757 Copy commit hash Bugfix: when running in export_features mode, museq used to skip the prediction. 20 Mar 2015 Diljot Grewal eb102233e63 Copy commit hash the makefile takes the python and boostpaths and input instead of hardcoded paths in the file. 20 Mar 2015 Diljot Grewal c6ff265bfa9 Copy commit hash MUT-351: implemented the export_features function and set the features_only flag to skip the prediction part. 20 Feb 2015 MUT-351 Diljot Grewal b69ccd50a7b Copy commit hash updated metadata.config 29 Jan 2015 Diljot Grewal 535b02f26a7 Copy commit hash minor bug fix 23 Jan 2015 Diljot Grewal 4994ee45ac8 Copy commit hash updated to version 4.3.3 Change log:
Fixed a bug in get_positions which caused museq to run on genome when interval ws a chromosome only
updated sklearn to 0.14.1 in install script
minor updates 19 Jan 2015 Diljot Grewal ca2ff663f09 Copy commit hash updated the version tags 24 Dec 2014 Diljot Grewal ced75beca1f Copy commit hash updated the background tuple calculation in the deep mode. updated the format for the manifest file. 24 Dec 2014 Diljot Grewal 79309130216 Copy commit hash updated the version tag 17 Dec 2014 
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