From 2d2a6c74d5a5a0c6962ae6a8c981fe0e8a179412 Mon Sep 17 00:00:00 2001
From: pdiakumis <peterdiakumis@gmail.com>
Date: Mon, 4 Dec 2023 19:36:26 +1100
Subject: [PATCH] dvc update tso data

---
 .dvc/config                                                  | 2 +-
 inst/extdata/tso/.gitignore                                  | 3 +++
 inst/extdata/tso/multiqc_data.json.dvc                       | 5 +++++
 .../sample705.AlignCollapseFusionCaller_metrics.json.gz.dvc  | 5 +++--
 inst/extdata/tso/sample705.TargetRegionCoverage.json.gz.dvc  | 5 +++--
 inst/extdata/tso/sample705.fragment_length_hist.json.gz.dvc  | 5 +++--
 inst/extdata/tso/sample705.msi.json.gz.dvc                   | 5 +++--
 inst/extdata/tso/sample705.tmb.json.gz.dvc                   | 5 +++--
 inst/extdata/tso/sample705_CombinedVariantOutput.tsv.dvc     | 4 ----
 .../tso/sample705_Failed_Exon_coverage_QC.json.gz.dvc        | 4 ----
 inst/extdata/tso/sample705_Failed_Exon_coverage_QC.txt.dvc   | 4 ----
 inst/extdata/tso/sample705_Fusions.csv.dvc                   | 5 +++--
 inst/extdata/tso/sample705_Fusions.json.gz.dvc               | 4 ----
 inst/extdata/tso/sample705_MergedSmallVariants.vcf.gz.dvc    | 5 +++++
 .../extdata/tso/sample705_MergedSmallVariants.vcf.gz.tbi.dvc | 5 +++++
 inst/extdata/tso/sample705_SampleAnalysisResults.json.gz.dvc | 5 +++--
 inst/extdata/tso/sample705_TMB_Trace.json.gz.dvc             | 4 ----
 inst/extdata/tso/sample705_TMB_Trace.tsv.dvc                 | 5 +++--
 18 files changed, 43 insertions(+), 37 deletions(-)
 create mode 100644 inst/extdata/tso/multiqc_data.json.dvc
 delete mode 100644 inst/extdata/tso/sample705_CombinedVariantOutput.tsv.dvc
 delete mode 100644 inst/extdata/tso/sample705_Failed_Exon_coverage_QC.json.gz.dvc
 delete mode 100644 inst/extdata/tso/sample705_Failed_Exon_coverage_QC.txt.dvc
 delete mode 100644 inst/extdata/tso/sample705_Fusions.json.gz.dvc
 create mode 100644 inst/extdata/tso/sample705_MergedSmallVariants.vcf.gz.dvc
 create mode 100644 inst/extdata/tso/sample705_MergedSmallVariants.vcf.gz.tbi.dvc
 delete mode 100644 inst/extdata/tso/sample705_TMB_Trace.json.gz.dvc

diff --git a/.dvc/config b/.dvc/config
index 543ec9d..4e4252d 100644
--- a/.dvc/config
+++ b/.dvc/config
@@ -1,4 +1,4 @@
 [core]
     remote = umccr_gdrive_dracarys
 ['remote "umccr_gdrive_dracarys"']
-    url = gdrive://1rScjhwdnekLQjqfyF4HyEIrBTVJmE_Dp
+    url = gdrive://1ht_3YUW769J8lzYS8edN85bQtOEdnKKx
diff --git a/inst/extdata/tso/.gitignore b/inst/extdata/tso/.gitignore
index cbae54a..600efcc 100644
--- a/inst/extdata/tso/.gitignore
+++ b/inst/extdata/tso/.gitignore
@@ -11,3 +11,6 @@
 /sample705_SampleAnalysisResults.json.gz
 /sample705_TMB_Trace.json.gz
 /sample705_TMB_Trace.tsv
+/sample705_MergedSmallVariants.vcf.gz
+/sample705_MergedSmallVariants.vcf.gz.tbi
+/multiqc_data.json
diff --git a/inst/extdata/tso/multiqc_data.json.dvc b/inst/extdata/tso/multiqc_data.json.dvc
new file mode 100644
index 0000000..d0ebae9
--- /dev/null
+++ b/inst/extdata/tso/multiqc_data.json.dvc
@@ -0,0 +1,5 @@
+outs:
+- md5: ca33a6a30d936647e5a5dd7d24f2dcf5
+  size: 364884
+  hash: md5
+  path: multiqc_data.json
diff --git a/inst/extdata/tso/sample705.AlignCollapseFusionCaller_metrics.json.gz.dvc b/inst/extdata/tso/sample705.AlignCollapseFusionCaller_metrics.json.gz.dvc
index b24d2f6..3891188 100644
--- a/inst/extdata/tso/sample705.AlignCollapseFusionCaller_metrics.json.gz.dvc
+++ b/inst/extdata/tso/sample705.AlignCollapseFusionCaller_metrics.json.gz.dvc
@@ -1,4 +1,5 @@
 outs:
-- md5: 824d5e363b8720b96972e29c9860e6e6
-  size: 2839
+- md5: 4e6609632f9dc57dae955889a87760e2
+  size: 6307
+  hash: md5
   path: sample705.AlignCollapseFusionCaller_metrics.json.gz
diff --git a/inst/extdata/tso/sample705.TargetRegionCoverage.json.gz.dvc b/inst/extdata/tso/sample705.TargetRegionCoverage.json.gz.dvc
index 4b1564f..65bbe72 100644
--- a/inst/extdata/tso/sample705.TargetRegionCoverage.json.gz.dvc
+++ b/inst/extdata/tso/sample705.TargetRegionCoverage.json.gz.dvc
@@ -1,4 +1,5 @@
 outs:
-- md5: da28ec32ef9b337a56350a48b9396538
-  size: 321
+- md5: 00a7667b4f32cbd352cec32c3f625ecb
+  size: 242
+  hash: md5
   path: sample705.TargetRegionCoverage.json.gz
diff --git a/inst/extdata/tso/sample705.fragment_length_hist.json.gz.dvc b/inst/extdata/tso/sample705.fragment_length_hist.json.gz.dvc
index d379e9e..6340ffd 100644
--- a/inst/extdata/tso/sample705.fragment_length_hist.json.gz.dvc
+++ b/inst/extdata/tso/sample705.fragment_length_hist.json.gz.dvc
@@ -1,4 +1,5 @@
 outs:
-- md5: 6c4f578fecc0eb6c4e4f0aef3e3b986c
-  size: 88655
+- md5: 22abb8f6217b42fb45925c90a675894b
+  size: 15842
+  hash: md5
   path: sample705.fragment_length_hist.json.gz
diff --git a/inst/extdata/tso/sample705.msi.json.gz.dvc b/inst/extdata/tso/sample705.msi.json.gz.dvc
index 27a49d0..e5a6a47 100644
--- a/inst/extdata/tso/sample705.msi.json.gz.dvc
+++ b/inst/extdata/tso/sample705.msi.json.gz.dvc
@@ -1,4 +1,5 @@
 outs:
-- md5: 0fa8625237fba976a072d6bf2f9df667
-  size: 542
+- md5: 4e657b82d0a1af72351970dcb30aad96
+  size: 581
+  hash: md5
   path: sample705.msi.json.gz
diff --git a/inst/extdata/tso/sample705.tmb.json.gz.dvc b/inst/extdata/tso/sample705.tmb.json.gz.dvc
index 41b22f5..d769360 100644
--- a/inst/extdata/tso/sample705.tmb.json.gz.dvc
+++ b/inst/extdata/tso/sample705.tmb.json.gz.dvc
@@ -1,4 +1,5 @@
 outs:
-- md5: 4f6bd85d75ce20f87fb50efc65f2908a
-  size: 479
+- md5: c39e93c4d34703419295bdc64313f4e1
+  size: 450
+  hash: md5
   path: sample705.tmb.json.gz
diff --git a/inst/extdata/tso/sample705_CombinedVariantOutput.tsv.dvc b/inst/extdata/tso/sample705_CombinedVariantOutput.tsv.dvc
deleted file mode 100644
index a6bcd24..0000000
--- a/inst/extdata/tso/sample705_CombinedVariantOutput.tsv.dvc
+++ /dev/null
@@ -1,4 +0,0 @@
-outs:
-- md5: 0be874bbb5d997d63a7c90cc4628ea4c
-  size: 188680
-  path: sample705_CombinedVariantOutput.tsv
diff --git a/inst/extdata/tso/sample705_Failed_Exon_coverage_QC.json.gz.dvc b/inst/extdata/tso/sample705_Failed_Exon_coverage_QC.json.gz.dvc
deleted file mode 100644
index 18cde23..0000000
--- a/inst/extdata/tso/sample705_Failed_Exon_coverage_QC.json.gz.dvc
+++ /dev/null
@@ -1,4 +0,0 @@
-outs:
-- md5: fb63b9328ddfe1c185025423a64b3c9a
-  size: 765
-  path: sample705_Failed_Exon_coverage_QC.json.gz
diff --git a/inst/extdata/tso/sample705_Failed_Exon_coverage_QC.txt.dvc b/inst/extdata/tso/sample705_Failed_Exon_coverage_QC.txt.dvc
deleted file mode 100644
index 1ef7187..0000000
--- a/inst/extdata/tso/sample705_Failed_Exon_coverage_QC.txt.dvc
+++ /dev/null
@@ -1,4 +0,0 @@
-outs:
-- md5: 19fdf89bca5422fd5bbb39c6ee2e9919
-  size: 1556
-  path: sample705_Failed_Exon_coverage_QC.txt
diff --git a/inst/extdata/tso/sample705_Fusions.csv.dvc b/inst/extdata/tso/sample705_Fusions.csv.dvc
index a421c31..e1c7248 100644
--- a/inst/extdata/tso/sample705_Fusions.csv.dvc
+++ b/inst/extdata/tso/sample705_Fusions.csv.dvc
@@ -1,4 +1,5 @@
 outs:
-- md5: 018ffe25ad052a196ecb8dc488eab686
-  size: 2269
+- md5: 3a3785dfa465c5c0bd9d4edbfc4e9d72
+  size: 1113
+  hash: md5
   path: sample705_Fusions.csv
diff --git a/inst/extdata/tso/sample705_Fusions.json.gz.dvc b/inst/extdata/tso/sample705_Fusions.json.gz.dvc
deleted file mode 100644
index 72a1f5b..0000000
--- a/inst/extdata/tso/sample705_Fusions.json.gz.dvc
+++ /dev/null
@@ -1,4 +0,0 @@
-outs:
-- md5: 1229486299781abc24148108fc84ebb8
-  size: 717
-  path: sample705_Fusions.json.gz
diff --git a/inst/extdata/tso/sample705_MergedSmallVariants.vcf.gz.dvc b/inst/extdata/tso/sample705_MergedSmallVariants.vcf.gz.dvc
new file mode 100644
index 0000000..36f4a56
--- /dev/null
+++ b/inst/extdata/tso/sample705_MergedSmallVariants.vcf.gz.dvc
@@ -0,0 +1,5 @@
+outs:
+- md5: 48ec9c0a040f7b4b21f7bf531b59d71b
+  size: 441141
+  hash: md5
+  path: sample705_MergedSmallVariants.vcf.gz
diff --git a/inst/extdata/tso/sample705_MergedSmallVariants.vcf.gz.tbi.dvc b/inst/extdata/tso/sample705_MergedSmallVariants.vcf.gz.tbi.dvc
new file mode 100644
index 0000000..daf60d5
--- /dev/null
+++ b/inst/extdata/tso/sample705_MergedSmallVariants.vcf.gz.tbi.dvc
@@ -0,0 +1,5 @@
+outs:
+- md5: e47edd3138a3bc29c96c4fd742d48440
+  size: 24715
+  hash: md5
+  path: sample705_MergedSmallVariants.vcf.gz.tbi
diff --git a/inst/extdata/tso/sample705_SampleAnalysisResults.json.gz.dvc b/inst/extdata/tso/sample705_SampleAnalysisResults.json.gz.dvc
index 28c0663..b9b8d75 100644
--- a/inst/extdata/tso/sample705_SampleAnalysisResults.json.gz.dvc
+++ b/inst/extdata/tso/sample705_SampleAnalysisResults.json.gz.dvc
@@ -1,4 +1,5 @@
 outs:
-- md5: cc4d0d65da5766daf0a6675aeb8e16f3
-  size: 167884
+- md5: a7a1214b3a886e2028a6e3c37c3e24c1
+  size: 115257
+  hash: md5
   path: sample705_SampleAnalysisResults.json.gz
diff --git a/inst/extdata/tso/sample705_TMB_Trace.json.gz.dvc b/inst/extdata/tso/sample705_TMB_Trace.json.gz.dvc
deleted file mode 100644
index 04ad806..0000000
--- a/inst/extdata/tso/sample705_TMB_Trace.json.gz.dvc
+++ /dev/null
@@ -1,4 +0,0 @@
-outs:
-- md5: 6f925733d3156adca0580df72e9df0a3
-  size: 72944
-  path: sample705_TMB_Trace.json.gz
diff --git a/inst/extdata/tso/sample705_TMB_Trace.tsv.dvc b/inst/extdata/tso/sample705_TMB_Trace.tsv.dvc
index 2c253a9..77f1551 100644
--- a/inst/extdata/tso/sample705_TMB_Trace.tsv.dvc
+++ b/inst/extdata/tso/sample705_TMB_Trace.tsv.dvc
@@ -1,4 +1,5 @@
 outs:
-- md5: 7e1968043c35f18bbd541cd8a5a2c453
-  size: 237841
+- md5: ccd776029107e41055becdaf271ad0c7
+  size: 178816
+  hash: md5
   path: sample705_TMB_Trace.tsv