diff --git a/files_larger_than_5MB b/files_larger_than_5MB new file mode 100644 index 0000000000000000000000000000000000000000..bc6dbbc3cbe460bb44f0779e4e48a1f3fcddeaa9 --- /dev/null +++ b/files_larger_than_5MB @@ -0,0 +1,55 @@ +runs/run1/01_kallisto_index +runs/kallisto_sleuth/run1/01_kallisto_index +runs/no_CWL_yet/kallisto_sleuth/run1/01_kallisto_index +runs/kallisto_collect/kallisto_sleuthObject.RData +runs/run1/03_kallisto_sleuthObject.RData +studies/TalinumGenomeDraft/resources/Talinum.gm.CDS.nt.fa +externals/Talinum.gm.CDS.nt.fa +runs/kallisto_collect/out/kallisto_sleuthObject.RData +runs/no_CWL_yet/kallisto_sleuth/run2/03_kallisto_sleuthObject.RData +runs/no_CWL_yet/kallisto_sleuth/run1/03_kallisto_sleuthObject.RData +runs/kallisto_sleuth/run2/03_kallisto_sleuthObject.RData +runs/kallisto_sleuth/run1/03_kallisto_sleuthObject.RData +runs/run1/01_kallisto_results/DB_165/abundance.h5 +runs/no_CWL_yet/kallisto_sleuth/run1/01_kallisto_results/DB_165/abundance.h5 +runs/kallisto_sleuth/run1/01_kallisto_results/DB_165/abundance.h5 +runs/kallisto_quant/kallisto_results/DB_165/abundance.h5 +runs/run1/01_kallisto_results/DB_163/abundance.h5 +runs/no_CWL_yet/kallisto_sleuth/run1/01_kallisto_results/DB_163/abundance.h5 +runs/kallisto_sleuth/run1/01_kallisto_results/DB_163/abundance.h5 +runs/kallisto_quant/kallisto_results/DB_163/abundance.h5 +runs/run1/01_kallisto_results/DB_099/abundance.h5 +runs/no_CWL_yet/kallisto_sleuth/run1/01_kallisto_results/DB_099/abundance.h5 +runs/kallisto_sleuth/run1/01_kallisto_results/DB_099/abundance.h5 +runs/kallisto_quant/kallisto_results/DB_099/abundance.h5 +runs/kallisto_quant/kallisto_results/DB_161_reC3MD_GTCCGC_L001_R1_001/abundance.h5 +runs/kallisto_quant/kallisto_results/DB_103_CAMMD_AGTCAA_L001_R1_001/abundance.h5 +runs/kallisto_quant/kallisto_results/DB_097_CAMMD_CAGATC_L001_R1_001/abundance.h5 +runs/run1/01_kallisto_results/DB_097/abundance.h5 +runs/no_CWL_yet/kallisto_sleuth/run1/01_kallisto_results/DB_097/abundance.h5 +runs/kallisto_sleuth/run1/01_kallisto_results/DB_097/abundance.h5 +runs/kallisto_quant/kallisto_results/DB_097/abundance.h5 +runs/kallisto_collect/kallisto_df.csv +runs/kallisto_sleuth/sleuth_dge.csv +runs/run1/03_kallisto_df.csv +runs/no_CWL_yet/kallisto_sleuth/run2/03_kallisto_df.csv +runs/no_CWL_yet/kallisto_sleuth/run1/03_kallisto_df.csv +runs/kallisto_sleuth/run2/03_kallisto_df.csv +runs/kallisto_sleuth/run1/03_kallisto_df.csv +runs/kallisto_quant/kallisto_results/DB_165_re-C3MD_GTGAAA_L002_R1_001/abundance.h5 +runs/run1/01_kallisto_results/DB_161/abundance.h5 +runs/no_CWL_yet/kallisto_sleuth/run1/01_kallisto_results/DB_161/abundance.h5 +runs/kallisto_sleuth/run1/01_kallisto_results/DB_161/abundance.h5 +runs/kallisto_quant/kallisto_results/DB_161/abundance.h5 +runs/kallisto_quant/kallisto_results/DB_099_CAMMD_CTTGTA_L001_R1_001/abundance.h5 +runs/kallisto_quant/kallisto_results/DB_163_reC3MD_GTGAAA_L001_R1_001/abundance.h5 +runs/run1/01_kallisto_results/DB_103/abundance.h5 +runs/no_CWL_yet/kallisto_sleuth/run1/01_kallisto_results/DB_103/abundance.h5 +runs/kallisto_sleuth/run1/01_kallisto_results/DB_103/abundance.h5 +runs/kallisto_quant/kallisto_results/DB_103/abundance.h5 +runs/kallisto_quant/kallisto_results_v48_anaconda/DB_163_reC3MD_GTGAAA_L001_R1_001/abundance.h5 +runs/kallisto_quant/kallisto_results_v48_anaconda/DB_161_reC3MD_GTCCGC_L001_R1_001/abundance.h5 +runs/kallisto_quant/kallisto_results_v48_anaconda/DB_165_re-C3MD_GTGAAA_L002_R1_001/abundance.h5 +runs/kallisto_quant/kallisto_results_v48_anaconda/DB_097_CAMMD_CAGATC_L001_R1_001/abundance.h5 +runs/kallisto_quant/kallisto_results_v48_anaconda/DB_103_CAMMD_AGTCAA_L001_R1_001/abundance.h5 +runs/kallisto_quant/kallisto_results_v48_anaconda/DB_099_CAMMD_CTTGTA_L001_R1_001/abundance.h5 diff --git a/git-analysis_2024-01-23T17:51:48/README b/git-analysis_2024-01-23T17:51:48/README new file mode 100644 index 0000000000000000000000000000000000000000..5e9e4efc4fc9ffbbb5fde13828fc0c5401c4b713 --- /dev/null +++ b/git-analysis_2024-01-23T17:51:48/README @@ -0,0 +1,70 @@ +== Overall Statistics == + Number of commits: 234 + Number of filenames: 1049 + Number of directories: 177 + Number of file extensions: 26 + + Total unpacked size (bytes): 2860995740 + Total packed size (bytes): 1978018454 + +== Caveats == +=== Sizes === +Packed size represents what size your repository would be if no +trees, commits, tags, or other metadata were included (though it may +fail to represent de-duplication; see below). It also represents the +current packing, which may be suboptimal if you haven't gc'ed for a +while. + +Unpacked size represents what size your repository would be if no +trees, commits, tags, or other metadata were included AND if no +files were packed; i.e., without delta-ing or compression. + +Both unpacked and packed sizes can be slightly misleading. Deleting +a blob from history not save as much space as the unpacked size, +because it is obviously normally stored in packed form. Also, +deleting a blob from history may not save as much space as its packed +size either, because another blob could be stored as a delta against +that blob, so when you remove one blob another blob's packed size may +grow. + +Also, the sum of the packed sizes can add up to more than the +repository size; if the same contents appeared in the repository in +multiple places, git will automatically de-dupe and store only one +copy, while the way sizes are added in this analysis adds the size +for each file path that has those contents. Further, if a file is +ever reverted to a previous version's contents, the previous +version's size will be counted multiple times in this analysis, even +though git will only store it once. + +=== Deletions === +Whether a file is deleted is not a binary quality, since it can be +deleted on some branches but still exist in others. Also, it might +exist in an old tag, but have been deleted in versions newer than +that. More thorough tracking could be done, including looking at +merge commits where one side of history deleted and the other modified, +in order to give a more holistic picture of deletions. However, that +algorithm would not only be more complex to implement, it'd also be +quite difficult to present and interpret by users. Since --analyze +is just about getting a high-level rough picture of history, it instead +implements the simplistic rule that is good enough for 98% of cases: + A file is marked as deleted if the last commit in the fast-export + stream that mentions the file lists it as deleted. +This makes it dependent on topological ordering, but generally gives +the "right" answer. + +=== Renames === +Renames share the same non-binary nature that deletions do, plus +additional challenges: + * If the renamed file is renamed again, instead of just two names for + a path you can have three or more. + * Rename pairs of the form (oldname, newname) that we consider to be + different names of the "same file" might only be valid over certain + commit ranges. For example, if a new commit reintroduces a file + named oldname, then new versions of oldname aren't the "same file" + anymore. We could try to portray this to the user, but it's easier + for the user to just break the pairing and only report unbroken + rename pairings to the user. + * The ability for users to rename files differently in different + branches means that our chains of renames will not necessarily be + linear but may branch out. + diff --git a/git-analysis_2024-01-23T17:51:48/blob-shas-and-paths.txt b/git-analysis_2024-01-23T17:51:48/blob-shas-and-paths.txt new file mode 100644 index 0000000000000000000000000000000000000000..6e05094b36bfd8c0b4d5757103a7b3ec0a5a17aa --- /dev/null +++ b/git-analysis_2024-01-23T17:51:48/blob-shas-and-paths.txt @@ -0,0 +1,784 @@ +=== Files by sha and associated pathnames in reverse size === +Format: sha, unpacked size, packed size, filename(s) object stored as + 6c7d4eb7e359a5c6bbeadcaae5b49b1662075846 750438441 566082725 [runs/kallisto_sleuth/run1/01_kallisto_index, runs/no_CWL_yet/kallisto_sleuth/run1/01_kallisto_index, runs/run1/01_kallisto_index] + 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+assays/Talinum_RNASeq_minimal/protocols/01_plant_material.md -> + studies/TalinumFacultativeCAM/protocols/01_plant_material.md + studies/TalinumFacultativeCAM/protocols/plant_material.md +assays/Talinum_RNASeq_minimal/protocols/02_RNAex_libraries.md -> + assays/Talinum_RNASeq_minimal/protocols/RNAex_libraries.md +externals/README.md -> + studies/TalinumGenomeDraft/README.md +externals/Talinum.gm.CDS.nt.fa -> + studies/TalinumGenomeDraft/resources/Talinum.gm.CDS.nt.fa +runs/kallisto_collect/isa.dataset.xlsx -> + runs/kallisto_collect/out/isa.dataset.xlsx +runs/kallisto_collect/kallisto_collect.yml -> + runs/kallisto_collect/run.yml +runs/kallisto_collect/kallisto_mappingStats.csv -> + runs/kallisto_collect/out/kallisto_mappingStats.csv +runs/kallisto_collect/kallisto_sleuthObject.RData -> + runs/kallisto_collect/out/kallisto_sleuthObject.RData +runs/kallisto_collect/kallisto_tpmMatrix.csv -> + runs/kallisto_collect/out/kallisto_tpmMatrix.csv +runs/kallisto_index/kallisto_index -> + runs/kallisto_index/out/kallisto_index +runs/kallisto_index/kallisto_index.yml -> + runs/kallisto_index/run.yml +runs/kallisto_quant/kallisto_quant.yml -> + runs/kallisto_quant/run.yml +runs/kallisto_quant/kallisto_results_v48_anaconda/DB_097_CAMMD_CAGATC_L001_R1_001/abundance.h5 -> + runs/kallisto_quant/kallisto_results/DB_097_CAMMD_CAGATC_L001_R1_001/abundance.h5 +runs/kallisto_quant/kallisto_results_v48_anaconda/DB_097_CAMMD_CAGATC_L001_R1_001/run_info.json -> + runs/kallisto_quant/kallisto_results/DB_097_CAMMD_CAGATC_L001_R1_001/run_info.json +runs/kallisto_quant/kallisto_results_v48_anaconda/DB_099_CAMMD_CTTGTA_L001_R1_001/abundance.h5 -> + runs/kallisto_quant/kallisto_results/DB_099_CAMMD_CTTGTA_L001_R1_001/abundance.h5 +runs/kallisto_quant/kallisto_results_v48_anaconda/DB_099_CAMMD_CTTGTA_L001_R1_001/run_info.json -> + runs/kallisto_quant/kallisto_results/DB_099_CAMMD_CTTGTA_L001_R1_001/run_info.json +runs/kallisto_quant/kallisto_results_v48_anaconda/DB_103_CAMMD_AGTCAA_L001_R1_001/abundance.h5 -> + runs/kallisto_quant/kallisto_results/DB_103_CAMMD_AGTCAA_L001_R1_001/abundance.h5 +runs/kallisto_quant/kallisto_results_v48_anaconda/DB_103_CAMMD_AGTCAA_L001_R1_001/run_info.json -> + runs/kallisto_quant/kallisto_results/DB_103_CAMMD_AGTCAA_L001_R1_001/run_info.json +runs/kallisto_quant/kallisto_results_v48_anaconda/DB_161_reC3MD_GTCCGC_L001_R1_001/abundance.h5 -> + runs/kallisto_quant/kallisto_results/DB_161_reC3MD_GTCCGC_L001_R1_001/abundance.h5 +runs/kallisto_quant/kallisto_results_v48_anaconda/DB_161_reC3MD_GTCCGC_L001_R1_001/run_info.json -> + runs/kallisto_quant/kallisto_results/DB_161_reC3MD_GTCCGC_L001_R1_001/run_info.json +runs/kallisto_quant/kallisto_results_v48_anaconda/DB_163_reC3MD_GTGAAA_L001_R1_001/abundance.h5 -> + runs/kallisto_quant/kallisto_results/DB_163_reC3MD_GTGAAA_L001_R1_001/abundance.h5 +runs/kallisto_quant/kallisto_results_v48_anaconda/DB_163_reC3MD_GTGAAA_L001_R1_001/run_info.json -> + runs/kallisto_quant/kallisto_results/DB_163_reC3MD_GTGAAA_L001_R1_001/run_info.json +runs/kallisto_quant/kallisto_results_v48_anaconda/DB_165_re-C3MD_GTGAAA_L002_R1_001/abundance.h5 -> + runs/kallisto_quant/kallisto_results/DB_165_re-C3MD_GTGAAA_L002_R1_001/abundance.h5 +runs/kallisto_quant/kallisto_results_v48_anaconda/DB_165_re-C3MD_GTGAAA_L002_R1_001/run_info.json -> + runs/kallisto_quant/kallisto_results/DB_165_re-C3MD_GTGAAA_L002_R1_001/run_info.json +runs/kallisto_sleuth/kallisto_sleuth.yml -> + runs/kallisto_sleuth/run.yml +runs/kallisto_sleuth/sleuth_dge.csv -> + runs/kallisto_sleuth/out/sleuth_dge.csv +runs/merged_isa_metadata/merged_isa.tsv -> + runs/merged_isa_metadata/out/merged_isa.tsv +runs/no_CWL_yet/kallisto_sleuth/run1/01_kallisto_results/DB_097/abundance.h5 -> + runs/kallisto_quant/kallisto_results/DB_097/abundance.h5 +runs/no_CWL_yet/kallisto_sleuth/run1/01_kallisto_results/DB_097/abundance.tsv -> + runs/kallisto_quant/kallisto_results/DB_097/abundance.tsv + runs/kallisto_quant/kallisto_results/DB_097_CAMMD_CAGATC_L001_R1_001/abundance.tsv +runs/no_CWL_yet/kallisto_sleuth/run1/01_kallisto_results/DB_097/run_info.json -> + runs/kallisto_quant/kallisto_results/DB_097/run_info.json +runs/no_CWL_yet/kallisto_sleuth/run1/01_kallisto_results/DB_099/abundance.h5 -> + runs/kallisto_quant/kallisto_results/DB_099/abundance.h5 +runs/no_CWL_yet/kallisto_sleuth/run1/01_kallisto_results/DB_099/abundance.tsv -> + runs/kallisto_quant/kallisto_results/DB_099/abundance.tsv + runs/kallisto_quant/kallisto_results/DB_099_CAMMD_CTTGTA_L001_R1_001/abundance.tsv +runs/no_CWL_yet/kallisto_sleuth/run1/01_kallisto_results/DB_099/run_info.json -> + runs/kallisto_quant/kallisto_results/DB_099/run_info.json +runs/no_CWL_yet/kallisto_sleuth/run1/01_kallisto_results/DB_103/abundance.h5 -> + runs/kallisto_quant/kallisto_results/DB_103/abundance.h5 +runs/no_CWL_yet/kallisto_sleuth/run1/01_kallisto_results/DB_103/abundance.tsv -> + runs/kallisto_quant/kallisto_results/DB_103/abundance.tsv + runs/kallisto_quant/kallisto_results/DB_103_CAMMD_AGTCAA_L001_R1_001/abundance.tsv +runs/no_CWL_yet/kallisto_sleuth/run1/01_kallisto_results/DB_103/run_info.json -> + runs/kallisto_quant/kallisto_results/DB_103/run_info.json +runs/no_CWL_yet/kallisto_sleuth/run1/01_kallisto_results/DB_161/abundance.h5 -> + runs/kallisto_quant/kallisto_results/DB_161/abundance.h5 +runs/no_CWL_yet/kallisto_sleuth/run1/01_kallisto_results/DB_161/abundance.tsv -> + runs/kallisto_quant/kallisto_results/DB_161/abundance.tsv + runs/kallisto_quant/kallisto_results/DB_161_reC3MD_GTCCGC_L001_R1_001/abundance.tsv +runs/no_CWL_yet/kallisto_sleuth/run1/01_kallisto_results/DB_161/run_info.json -> + runs/kallisto_quant/kallisto_results/DB_161/run_info.json +runs/no_CWL_yet/kallisto_sleuth/run1/01_kallisto_results/DB_163/abundance.h5 -> + runs/kallisto_quant/kallisto_results/DB_163/abundance.h5 +runs/no_CWL_yet/kallisto_sleuth/run1/01_kallisto_results/DB_163/abundance.tsv -> + runs/kallisto_quant/kallisto_results/DB_163/abundance.tsv + runs/kallisto_quant/kallisto_results/DB_163_reC3MD_GTGAAA_L001_R1_001/abundance.tsv +runs/no_CWL_yet/kallisto_sleuth/run1/01_kallisto_results/DB_163/run_info.json -> + runs/kallisto_quant/kallisto_results/DB_163/run_info.json +runs/no_CWL_yet/kallisto_sleuth/run1/01_kallisto_results/DB_165/abundance.h5 -> + runs/kallisto_quant/kallisto_results/DB_165/abundance.h5 +runs/no_CWL_yet/kallisto_sleuth/run1/01_kallisto_results/DB_165/abundance.tsv -> + runs/kallisto_quant/kallisto_results/DB_165/abundance.tsv + runs/kallisto_quant/kallisto_results/DB_165_re-C3MD_GTGAAA_L002_R1_001/abundance.tsv +runs/no_CWL_yet/kallisto_sleuth/run1/01_kallisto_results/DB_165/run_info.json -> + runs/kallisto_quant/kallisto_results/DB_165/run_info.json +runs/run1/01_kallisto_results/DB_097/abundance.h5 -> + runs/kallisto_sleuth/run1/01_kallisto_results/DB_097/abundance.h5 +runs/run1/01_kallisto_results/DB_097/abundance.tsv -> + runs/kallisto_sleuth/run1/01_kallisto_results/DB_097/abundance.tsv +runs/run1/01_kallisto_results/DB_097/run_info.json -> + runs/kallisto_sleuth/run1/01_kallisto_results/DB_097/run_info.json +runs/run1/01_kallisto_results/DB_099/abundance.h5 -> + runs/kallisto_sleuth/run1/01_kallisto_results/DB_099/abundance.h5 +runs/run1/01_kallisto_results/DB_099/abundance.tsv -> + runs/kallisto_sleuth/run1/01_kallisto_results/DB_099/abundance.tsv +runs/run1/01_kallisto_results/DB_099/run_info.json -> + runs/kallisto_sleuth/run1/01_kallisto_results/DB_099/run_info.json +runs/run1/01_kallisto_results/DB_103/abundance.h5 -> + runs/kallisto_sleuth/run1/01_kallisto_results/DB_103/abundance.h5 +runs/run1/01_kallisto_results/DB_103/abundance.tsv -> + runs/kallisto_sleuth/run1/01_kallisto_results/DB_103/abundance.tsv +runs/run1/01_kallisto_results/DB_103/run_info.json -> + runs/kallisto_sleuth/run1/01_kallisto_results/DB_103/run_info.json +runs/run1/01_kallisto_results/DB_161/abundance.h5 -> + runs/kallisto_sleuth/run1/01_kallisto_results/DB_161/abundance.h5 +runs/run1/01_kallisto_results/DB_161/abundance.tsv -> + runs/kallisto_sleuth/run1/01_kallisto_results/DB_161/abundance.tsv +runs/run1/01_kallisto_results/DB_161/run_info.json -> + runs/kallisto_sleuth/run1/01_kallisto_results/DB_161/run_info.json +runs/run1/01_kallisto_results/DB_163/abundance.h5 -> + runs/kallisto_sleuth/run1/01_kallisto_results/DB_163/abundance.h5 +runs/run1/01_kallisto_results/DB_163/abundance.tsv -> + runs/kallisto_sleuth/run1/01_kallisto_results/DB_163/abundance.tsv +runs/run1/01_kallisto_results/DB_163/run_info.json -> + runs/kallisto_sleuth/run1/01_kallisto_results/DB_163/run_info.json +runs/run1/01_kallisto_results/DB_165/abundance.h5 -> + runs/kallisto_sleuth/run1/01_kallisto_results/DB_165/abundance.h5 +runs/run1/01_kallisto_results/DB_165/abundance.tsv -> + runs/kallisto_sleuth/run1/01_kallisto_results/DB_165/abundance.tsv +runs/run1/01_kallisto_results/DB_165/run_info.json -> + runs/kallisto_sleuth/run1/01_kallisto_results/DB_165/run_info.json +runs/run1/03_kallisto_df.csv -> + runs/kallisto_sleuth/run1/03_kallisto_df.csv +runs/run1/03_kallisto_mappingStats.csv -> + runs/kallisto_sleuth/run1/03_kallisto_mappingStats.csv +runs/run1/03_kallisto_sleuthObject.RData -> + runs/kallisto_sleuth/run1/03_kallisto_sleuthObject.RData +runs/run1/03_kallisto_tpmMatrix.csv -> + runs/kallisto_sleuth/run1/03_kallisto_tpmMatrix.csv +runs/run1/04_sleuth_dge.csv -> + runs/kallisto_sleuth/run1/04_sleuth_dge.csv +runs/run1/05_shinyPrep.RData -> + runs/kallisto_sleuth/run1/05_shinyPrep.RData +runs/run1/isa.run.xlsx -> + runs/kallisto_sleuth/run1/isa.run.xlsx +runs/shiny_prep/shiny_prep.yml -> + runs/shiny_prep/run.yml +workflows/01_KallistoQuant.sh -> + workflows/kallisto_sleuth/01_KallistoQuant.sh +workflows/02_InstallPackages.R -> + workflows/kallisto_sleuth/02_InstallPackages.R +workflows/03_KallistoCollect.R -> + workflows/kallisto_sleuth/03_KallistoCollect.R +workflows/04_Sleuth.R -> + workflows/kallisto_sleuth/04_Sleuth.R +workflows/05_plot_shinyPrep.R -> + workflows/kallisto_sleuth/05_plot_shinyPrep.R +workflows/06_plot_shinyApp.Rmd -> + workflows/plot_shinyApp.Rmd + workflows/shiny_plots.Rmd + workflows/shiny_prep/shiny_plots.Rmd + runs/shiny_plots.Rmd +workflows/_dependencies/install_cwl.md -> + workflows/install_dependencies/install_cwl.md +workflows/_dependencies/install_kallisto.md -> + workflows/install_dependencies/install_kallisto.md +workflows/kallisto_collect.R -> + workflows/kallisto_collect/kallisto_collect.R +workflows/kallisto_collect.cwl -> + workflows/kallisto_collect/workflow.cwl +workflows/kallisto_index.cwl -> + workflows/kallisto_index/workflow.cwl +workflows/kallisto_index.sh -> + workflows/kallisto_index/kallisto_index.sh +workflows/kallisto_quant.cwl -> + workflows/kallisto_quant/workflow.cwl +workflows/kallisto_quant.sh -> + workflows/kallisto_quant/kallisto_quant.sh +workflows/kallisto_sleuth.R -> + workflows/kallisto_sleuth/kallisto_sleuth.R +workflows/kallisto_sleuth.cwl -> + workflows/kallisto_sleuth/workflow.cwl +workflows/merge_isa_metadata.R -> + workflows/merge_isa_metadata/merge_isa_metadata.R +workflows/merge_isa_metadata.cwl -> + workflows/merge_isa_metadata/workflow.cwl +workflows/merge_isa_metadata.yml -> + runs/merged_isa_metadata/merge_isa_metadata.yml + runs/merged_isa_metadata/run.yml +workflows/shiny_prep.R -> + workflows/shiny_prep/shiny_prep.R +workflows/shiny_prep.cwl -> + workflows/shiny_prep/workflow.cwl diff --git a/git-analysis_2024-01-23T18:10:28/README b/git-analysis_2024-01-23T18:10:28/README new file mode 100644 index 0000000000000000000000000000000000000000..1d7c17617bebda3b27ef726984e87c54e8ecb5b4 --- /dev/null +++ b/git-analysis_2024-01-23T18:10:28/README @@ -0,0 +1,70 @@ +== Overall Statistics == + Number of commits: 138 + Number of filenames: 997 + Number of directories: 177 + Number of file extensions: 24 + + Total unpacked size (bytes): 103737998 + Total packed size (bytes): 39486084 + +== Caveats == +=== Sizes === +Packed size represents what size your repository would be if no +trees, commits, tags, or other metadata were included (though it may +fail to represent de-duplication; see below). It also represents the +current packing, which may be suboptimal if you haven't gc'ed for a +while. + +Unpacked size represents what size your repository would be if no +trees, commits, tags, or other metadata were included AND if no +files were packed; i.e., without delta-ing or compression. + +Both unpacked and packed sizes can be slightly misleading. Deleting +a blob from history not save as much space as the unpacked size, +because it is obviously normally stored in packed form. Also, +deleting a blob from history may not save as much space as its packed +size either, because another blob could be stored as a delta against +that blob, so when you remove one blob another blob's packed size may +grow. + +Also, the sum of the packed sizes can add up to more than the +repository size; if the same contents appeared in the repository in +multiple places, git will automatically de-dupe and store only one +copy, while the way sizes are added in this analysis adds the size +for each file path that has those contents. Further, if a file is +ever reverted to a previous version's contents, the previous +version's size will be counted multiple times in this analysis, even +though git will only store it once. + +=== Deletions === +Whether a file is deleted is not a binary quality, since it can be +deleted on some branches but still exist in others. Also, it might +exist in an old tag, but have been deleted in versions newer than +that. More thorough tracking could be done, including looking at +merge commits where one side of history deleted and the other modified, +in order to give a more holistic picture of deletions. However, that +algorithm would not only be more complex to implement, it'd also be +quite difficult to present and interpret by users. Since --analyze +is just about getting a high-level rough picture of history, it instead +implements the simplistic rule that is good enough for 98% of cases: + A file is marked as deleted if the last commit in the fast-export + stream that mentions the file lists it as deleted. +This makes it dependent on topological ordering, but generally gives +the "right" answer. + +=== Renames === +Renames share the same non-binary nature that deletions do, plus +additional challenges: + * If the renamed file is renamed again, instead of just two names for + a path you can have three or more. + * Rename pairs of the form (oldname, newname) that we consider to be + different names of the "same file" might only be valid over certain + commit ranges. For example, if a new commit reintroduces a file + named oldname, then new versions of oldname aren't the "same file" + anymore. We could try to portray this to the user, but it's easier + for the user to just break the pairing and only report unbroken + rename pairings to the user. + * The ability for users to rename files differently in different + branches means that our chains of renames will not necessarily be + linear but may branch out. + diff --git a/git-analysis_2024-01-23T18:10:28/blob-shas-and-paths.txt b/git-analysis_2024-01-23T18:10:28/blob-shas-and-paths.txt new file mode 100644 index 0000000000000000000000000000000000000000..56c14d70a4a2f53c92ae1015e48bf96410f08238 --- /dev/null +++ b/git-analysis_2024-01-23T18:10:28/blob-shas-and-paths.txt @@ -0,0 +1,756 @@ +=== Files by sha and associated pathnames in reverse size === +Format: sha, unpacked size, packed size, filename(s) object stored as + 258a091981fee5ee5389d9e76ca25e2a237768b8 1947155 1746581 runs/shiny_prep/shiny_prep.RData + e05d66658d5b95026e2731cf8c6ac993fe04f4c2 1947166 1746540 [runs/kallisto_sleuth/run1/05_shinyPrep.RData, 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runs/kallisto_sleuth/run1/01_kallisto_results/DB_103/run_info.json +runs/run1/01_kallisto_results/DB_161/abundance.tsv -> + runs/kallisto_sleuth/run1/01_kallisto_results/DB_161/abundance.tsv +runs/run1/01_kallisto_results/DB_161/run_info.json -> + runs/kallisto_sleuth/run1/01_kallisto_results/DB_161/run_info.json +runs/run1/01_kallisto_results/DB_163/abundance.tsv -> + runs/kallisto_sleuth/run1/01_kallisto_results/DB_163/abundance.tsv +runs/run1/01_kallisto_results/DB_163/run_info.json -> + runs/kallisto_sleuth/run1/01_kallisto_results/DB_163/run_info.json +runs/run1/01_kallisto_results/DB_165/abundance.tsv -> + runs/kallisto_sleuth/run1/01_kallisto_results/DB_165/abundance.tsv +runs/run1/01_kallisto_results/DB_165/run_info.json -> + runs/kallisto_sleuth/run1/01_kallisto_results/DB_165/run_info.json +runs/run1/03_kallisto_mappingStats.csv -> + runs/kallisto_sleuth/run1/03_kallisto_mappingStats.csv +runs/run1/03_kallisto_tpmMatrix.csv -> + runs/kallisto_sleuth/run1/03_kallisto_tpmMatrix.csv +runs/run1/04_sleuth_dge.csv -> + runs/kallisto_sleuth/run1/04_sleuth_dge.csv +runs/run1/05_shinyPrep.RData -> + runs/kallisto_sleuth/run1/05_shinyPrep.RData +runs/run1/isa.run.xlsx -> + runs/kallisto_sleuth/run1/isa.run.xlsx +runs/shiny_prep/shiny_prep.yml -> + runs/shiny_prep/run.yml +workflows/01_KallistoQuant.sh -> + workflows/kallisto_sleuth/01_KallistoQuant.sh +workflows/02_InstallPackages.R -> + workflows/kallisto_sleuth/02_InstallPackages.R +workflows/03_KallistoCollect.R -> + workflows/kallisto_sleuth/03_KallistoCollect.R +workflows/04_Sleuth.R -> + workflows/kallisto_sleuth/04_Sleuth.R +workflows/05_plot_shinyPrep.R -> + workflows/kallisto_sleuth/05_plot_shinyPrep.R +workflows/06_plot_shinyApp.Rmd -> + workflows/plot_shinyApp.Rmd + workflows/shiny_plots.Rmd + workflows/shiny_prep/shiny_plots.Rmd + runs/shiny_plots.Rmd +workflows/_dependencies/install_cwl.md -> + workflows/install_dependencies/install_cwl.md +workflows/_dependencies/install_kallisto.md -> + workflows/install_dependencies/install_kallisto.md +workflows/kallisto_collect.R -> + workflows/kallisto_collect/kallisto_collect.R +workflows/kallisto_collect.cwl -> + workflows/kallisto_collect/workflow.cwl +workflows/kallisto_index.cwl -> + workflows/kallisto_index/workflow.cwl +workflows/kallisto_index.sh -> + workflows/kallisto_index/kallisto_index.sh +workflows/kallisto_quant.cwl -> + workflows/kallisto_quant/workflow.cwl +workflows/kallisto_quant.sh -> + workflows/kallisto_quant/kallisto_quant.sh +workflows/kallisto_sleuth.R -> + workflows/kallisto_sleuth/kallisto_sleuth.R +workflows/kallisto_sleuth.cwl -> + workflows/kallisto_sleuth/workflow.cwl +workflows/merge_isa_metadata.R -> + workflows/merge_isa_metadata/merge_isa_metadata.R +workflows/merge_isa_metadata.cwl -> + workflows/merge_isa_metadata/workflow.cwl +workflows/merge_isa_metadata.yml -> + runs/merged_isa_metadata/merge_isa_metadata.yml + 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