From a458537e6bd607160ed7e902cd058f5ea2dcbe57 Mon Sep 17 00:00:00 2001
From: Jaeyoung Chun <jaeyoung.chun@gmail.com>
Date: Sat, 26 Mar 2022 08:58:44 -0400
Subject: [PATCH 1/4] Set version to 0.2.11

---
 src/seqc/version.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/seqc/version.py b/src/seqc/version.py
index 6232f7a..5635676 100644
--- a/src/seqc/version.py
+++ b/src/seqc/version.py
@@ -1 +1 @@
-__version__ = "0.2.10"
+__version__ = "0.2.11"

From ac62a6c32bea34504b3e6b3e384377e0585c52e3 Mon Sep 17 00:00:00 2001
From: Jaeyoung Chun <jaeyoung.chun@gmail.com>
Date: Sat, 26 Mar 2022 08:58:58 -0400
Subject: [PATCH 2/4] Update docs

---
 README.md            | 2 +-
 docs/README.md       | 8 ++++----
 docs/install-SUSE.md | 6 +++---
 3 files changed, 8 insertions(+), 8 deletions(-)

diff --git a/README.md b/README.md
index 306641f..2fefc38 100644
--- a/README.md
+++ b/README.md
@@ -38,7 +38,7 @@ To process data locally using SEQC, you must install the <a href=https://github.
 Once all dependencies have been installed, SEQC can be installed by running:
 
 ```bash
-export SEQC_VERSION="0.2.10"
+export SEQC_VERSION="0.2.11"
 wget https://github.com/hisplan/seqc/archive/v${SEQC_VERSION}.tar.gz
 tar xvzf v${SEQC_VERSION}.tar.gz
 cd seqc-${SEQC_VERSION}
diff --git a/docs/README.md b/docs/README.md
index 14a4bf3..6a3c936 100644
--- a/docs/README.md
+++ b/docs/README.md
@@ -8,9 +8,9 @@
 
 ## Generating Reference Packages
 
-This generates a reference package (STAR index and GTF) using SEQC v0.2.10.
+This generates a reference package (STAR index and GTF) using SEQC.
 
-- Ensembl 86
+- Ensembl 85
 - Gene annotation file that contains only the reference chromosomes (no scaffolds, no patches)
 - Only these biotypes: 'protein_coding', 'lincRNA', 'IG_V_gene', 'IG_C_gene', 'IG_J_gene', 'TR_C_gene', 'TR_J_gene', 'TR_V_gene', 'TR_D_gene', 'IG_D_gene'
 - Not passing anything to `--additional-id-types`
@@ -22,7 +22,7 @@ This generates a reference package (STAR index and GTF) using SEQC v0.2.10.
 SEQC index \
     -o homo_sapiens \
     -f homo_sapiens \
-    --ensemble-release 93 \
+    --ensemble-release 85 \
     --valid-biotypes protein_coding lincRNA antisense IG_V_gene IG_D_gene IG_J_gene IG_C_gene TR_V_gene TR_D_gene TR_J_gene TR_C_gene \
     --read-length 101 \
     --folder ./test-data/index/ \
@@ -35,7 +35,7 @@ SEQC index \
 SEQC index \
     -o homo_sapiens \
     -f homo_sapiens \
-    --ensemble-release 93 \
+    --ensemble-release 85 \
     --valid-biotypes protein_coding lincRNA antisense IG_V_gene IG_D_gene IG_J_gene IG_C_gene TR_V_gene TR_D_gene TR_J_gene TR_C_gene \
     --read-length 101 \
     --upload-prefix s3://dp-lab-test/seqc/index/86/ \
diff --git a/docs/install-SUSE.md b/docs/install-SUSE.md
index eb5b2b9..171b600 100644
--- a/docs/install-SUSE.md
+++ b/docs/install-SUSE.md
@@ -43,8 +43,8 @@ conda install -c bioconda star
 ## Install SEQC
 
 ```
-wget https://github.com/dpeerlab/seqc/archive/v0.2.10.tar.gz
-tar xvzf v0.2.10.tar.gz
-cd seqc-0.2.10/
+wget https://github.com/dpeerlab/seqc/archive/v0.2.11.tar.gz
+tar xvzf v0.2.11.tar.gz
+cd seqc-0.2.11/
 pip install .
 ```

From abc7bacaa33bcfc967aff447c7e72a9809fd3abb Mon Sep 17 00:00:00 2001
From: Jaeyoung Chun <jaeyoung.chun@gmail.com>
Date: Sat, 26 Mar 2022 08:59:25 -0400
Subject: [PATCH 3/4] Add 10x-compatible matrix to the output list

---
 src/seqc/core/run.py | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/src/seqc/core/run.py b/src/seqc/core/run.py
index 810e013..94c10ba 100644
--- a/src/seqc/core/run.py
+++ b/src/seqc/core/run.py
@@ -533,6 +533,9 @@ def create_read_array(
             args.output_prefix + "_sparse_molecule_counts.mtx",
             args.output_prefix + "_sparse_counts_barcodes.csv",
             args.output_prefix + "_sparse_counts_genes.csv",
+            "raw_feature_bc_matrix/matrix.mtx.gz",
+            "raw_feature_bc_matrix/barcodes.tsv.gz",
+            "raw_feature_bc_matrix/features.tsv.gz",
         ]
 
         if os.path.exists(args.output_prefix + "_cb-correction.csv.gz"):

From 8c37e93c21244bf4d07d920126a396e3f4e604cb Mon Sep 17 00:00:00 2001
From: Jaeyoung Chun <jaeyoung.chun@gmail.com>
Date: Sat, 26 Mar 2022 09:01:41 -0400
Subject: [PATCH 4/4] Add --force-glacier-transfer

---
 src/seqc/io.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/seqc/io.py b/src/seqc/io.py
index 69026c2..59c8a4f 100644
--- a/src/seqc/io.py
+++ b/src/seqc/io.py
@@ -136,7 +136,7 @@ def download_awscli(cls, link, prefix='./', overwrite=True, recursive=False):
                 'provided link %s was a prefix but download was not called recursively. '
                 'Please provide a filename or download recursively.' % link)
 
-        cmd = 'aws s3 cp %s %s' % (link, prefix)
+        cmd = 'aws s3 cp --force-glacier-transfer %s %s' % (link, prefix)
         if recursive:
             cmd += ' --recursive'