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Created with Raphaël 2.2.018Sep1712112Aug131Jul262524212018171311106427Jun262120191817151413125430May292625242322201918Add options --merge_distance, --ignore_haplotypes, and --min_cell_count.Add options --merge_distance, --ignore_haplotypes, and --min_cell_count.Add options --merge_distance, --ignore_haplotypes, and --min_cell_count.Add options --merge_distance, --ignore_haplotypes, and --min_cell_count.Run StrandPhaseR separately for each segmentation parameter set; this is necessary since the segmentation calls affect strand states / SCE calls.Run StrandPhaseR separately for each segmentation parameter set; this is necessary since the segmentation calls affect strand states / SCE calls.Run StrandPhaseR separately for each segmentation parameter set; this is necessary since the segmentation calls affect strand states / SCE calls.Run StrandPhaseR separately for each segmentation parameter set; this is necessary since the segmentation calls affect strand states / SCE calls.Use local script to plot SV calls and mark complex regions.Use local script to plot SV calls and mark complex regions.Use local script to plot SV calls and mark complex regions.Use local script to plot SV calls and mark complex regions.Add option to plot track with complex regionsAdd option to plot track with complex regionsAdd option to plot track with complex regionsAdd option to plot track with complex regionsScript to plot SV calls, copied from github.com:friendsofstrandseq/mosaicatcher/R/chrom.R (having it here allows local, coordinated changes)Script to plot SV calls, copied from github.com:friendsofstrandseq/mosaicatcher/R/chrom.R (having it here allows local, coordinated changes)Script to plot SV calls, copied from github.com:friendsofstrandseq/mosaicatcher/R/chrom.R (having it here allows local, coordinated changes)Script to plot SV calls, copied from github.com:friendsofstrandseq/mosaicatcher/R/chrom.R (having it here allows local, coordinated changes)chenged an argument name for consistencychenged an argument name for consistencychenged an argument name for consistencychenged an argument name for consistencyAlso consider sv type when computing number of unique calls. Slightly changed log output.Also consider sv type when computing number of unique calls. Slightly changed log output.Also consider sv type when computing number of unique calls. Slightly changed log output.Also consider sv type when computing number of unique calls. Slightly changed log output.Retain logs and produce aggregate statistics. Also fix tabs/spaces.Retain logs and produce aggregate statistics. Also fix tabs/spaces.Retain logs and produce aggregate statistics. Also fix tabs/spaces.Retain logs and produce aggregate statistics. Also fix tabs/spaces.Evaluate different parameter settings, including different modes to select a segmentation.Evaluate different parameter settings, including different modes to select a segmentation.Evaluate different parameter settings, including different modes to select a segmentation.Evaluate different parameter settings, including different modes to select a segmentation.Script to collect callset statistics and to compare to ground truthScript to collect callset statistics and to compare to ground truthScript to collect callset statistics and to compare to ground truthScript to collect callset statistics and to compare to ground truth