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- big/cassava.dsgm+3
- big/cassava.vcf+3
- big/pedigree_table+3
- cassava_dsout_agmr_histogram_480x360.png
- data/5krandom_pedigrees+5.0k
- data/pedtable3col+8.2k
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- lib/Gnuplot_plot.pm+248
- lib/Hdata.pm+190
- lib/Histograms.pm+815
- lib/Plot.pm+125
- moose/bin/analyze_ppout.pl+68
- moose/bin/analyze_triples.pl+156
- moose/bin/grandparents.pl+42
- moose/bin/phased_parents.pl+527
- moose/bin/phpars.pl+508
- moose/bin/random_pedigrees.pl+53
- moose/bin/sel_par_progs.pl+31
- moose/bin/vcf2gts_phased.pl+222
- moose/lib/Chromosome.pm+52
- moose/lib/Cluster1d.pm+74-81
- moose/lib/Marker.pm+32
- other/compare_2file_agmrs.pl
- other/dosage_matrix_info.pl+62
- other/fix_pedigree_table.pl+57
- other/nndists.pl
- other/select_accessions_by_ids.pl+44
- other/triples_3_cases.pl+102
- other/uniquify_pedigree_file.pl+107
- other/vcf_acc_subset.pl+80
- other/vcf_format_check.pl+117
- src/agmr_cluster.pl-218
- src/best_triples.pl-69
- src/bt_best_vs_nextbest.pl-30
- src/bt_category_counts.pl-97
- src/closest_pairs.pl-19
- src/clusterer.pl+503-368
- src/d_vs_md.pl-26
- src/dosage_from_allele_depths.pl-32
- src/duplicate_finder.pl+244-100
- src/duplicate_search.c+671-316
- src/find_parents.c+568-160
- src/gtset.c+1.3k-415
- src/gwas/Manhattan.pl+92
- src/gwas/dsgs2ped.pl+48
- src/gwas/fn_vs_fp.pl+46
- src/gwas/manhattan.gnuplot+43
- src/gwas/plnkout2dsout.pl+2-2
- src/gwas/rand_dupe_no_dupe.pl+238
- src/gwas/sim_gwas_dupes_vs_nodupes.pl+115
- src/gwas/simmultiphenotypes.pl+154
- src/histogram.pl+212
- src/maf_freqs.pl-66
- src/makefile+15-14
- src/multipedigrees.pl-48
- src/n01_3etc.pl-102
- src/nxy_z.pl-137
- src/old/DSvcf2gts.pl+271
- src/old/bad_accessions_begone.pl
- src/old/find_parent_candidates.c+1-1
- src/old/pedigree_test.c+75-113
- src/old/plnkout_to_dsout.c+171
- src/old/remove_duplicates.pl+4-4
- src/old/vcf2gts.pl+70-57
- src/pedigree.c+646-1.2k
- src/pedigree_ids.pl-12
- src/progeny_parents_both.pl-70
- src/pt_vs_fp.pl-208
- src/ptfpbt.pl-75
- src/select_accessions_by_ids.pl-30
- src/triples_3_cases.pl-87
- src/uniquify.pl+229-199
- src/uniquify_pedigree_file.pl-54
- src/various.c+44-1
- src/vcf_data.pl-17
- src/vcf_thru_find_parents.pl+92
- src/vcf_to_dsgm.c+979
- src/vcf_to_gts.c-514
- src/vect.c+164-17
- src/xvcf.pl-13
- testing/alt0.fpout_std+7.6k
- testing/alt1.fpout_std+8.1k
- testing/alt2.fpout_std+7.6k
- testing/alt3.fpout_std+8.1k
- testing/dstest.pl+38
- testing/fpout_compare.pl+109
- testing/noped.fpout_std+8.1k
- testing/test_find_parents.pl+112
- util/quadrants.pl+59
- util/sel_columns.pl+16
- util/select_random_columns.pl+37
- util/sort_by_col.pl+19
- util/venn_lines.pl+73
- util/words_per_line.pl+53
- R/Spatial_Correction.R+77-16
- R/spatial_correlation_check.R+1-1
- js/source/legacy/CXGN/List.js+15-5
- js/source/legacy/d3/graphers/nirsDataLineGraph.js+393
- lib/CXGN/PhenotypingTrial.pm+53-1
- lib/CXGN/Project.pm+34-33
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- lib/SGN/Controller/AJAX/FieldBook.pm+142-138
- lib/SGN/Controller/AJAX/HTMLSelect.pm+21-3
- lib/SGN/Controller/AJAX/SpatialModel.pm+37-4
- lib/SGN/Controller/AJAX/TrialMetadata.pm+48-15
- lib/SGN/Controller/BreedersToolbox/Download.pm+58-1
- lib/SGN/Controller/FieldBook.pm+36-1
- mason/breeders_toolbox/trial.mas+28-5
- mason/breeders_toolbox/trial/design_section.mas+8
- mason/breeders_toolbox/trial/edit_fieldMap.mas+94-57
- mason/breeders_toolbox/trial/phenotype_heatmap.mas+73-72
- mason/breeders_toolbox/trial/summary_stock_entries.mas+59
- mason/breeders_toolbox/trial/trial_nirs_data.mas+341
- mason/breeders_toolbox/upload_nirs_spreadsheet_dialogs.mas+1-1
- mason/fieldbook/home.mas+65-29
- mason/page/detail_page_2_col_section.mas+3
- mason/tools/high_dimensional_phenotypes/upload_high_dim_spreadsheet_dialogs.mas+1
- mason/tools/image_analysis.mas+11-7
- mason/tools/nirs/nirs_analysis_train_dialogs.mas+1
- sgn.conf+1-1
- t/selenium2/01_list/list_groups.t+5
- t/unit_fixture/CXGN/Trial/AddPlantsandTissueSamplesToTrial.t+38
- t/unit_mech/AJAX/_BrAPIv2_phenotyping.t+188
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