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changelog
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changelog
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Version 0.81, 6/14/2018
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-PPmanhat will now perform z-transformation on values with the -z argument
-Minor bug fixes and additional error checking
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Version 0.8, 5/17/2018
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-Added the ability to use a VCF with SNP locations and skip variant calling
-Added the ability to only perform alignment with PPalign
-Fixed a bug in PPanalyze that was improperly filtering the coverage tables
-Can now use single-end reads; PPalign will automatically detect if reads are SE based on samplelist
-A full and complete frequency table are no longer produced in PPalign. Now, a single frequency table that represents the old frequency table is produced (.fz)
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Version 0.76, 4/10/2018
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Added new utility bash and R scripts for additional analyses:
- PPmanhat, with r_plotter.R
- PPrunls, with r_localscore.R
- PPrunflk, with r_FLKu.R
- PPruncmh
- PPsubset
-Updated example documentation
-Fixed a common error in Rscript due to antiquated notation in MaxtrixStats
-Added a check for mkfifo in PPalign and PPstats
-Changed certain instances of awk to gawk which fixed memory issues for some users
-Added PCA to r_structure.R
-PPalign no longer writes full temporary mpileup, instead uses process substitution to filter while creating mpileups
-Set pipefail for scripts to exit upon any errors
-Additional minor bug fixes