From fd37466dd399653996da44b985a4b3b3b7ffcde6 Mon Sep 17 00:00:00 2001
From: Jody Phelan <jody.phelan@lshtm.ac.uk>
Date: Mon, 24 Feb 2025 15:56:53 +0000
Subject: [PATCH 1/5] bump version

---
 tbprofiler/__init__.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/tbprofiler/__init__.py b/tbprofiler/__init__.py
index 7a9db6b..083c3c1 100644
--- a/tbprofiler/__init__.py
+++ b/tbprofiler/__init__.py
@@ -9,4 +9,4 @@
 from .plugins import *
 from .rules import *
 
-__version__ = "6.6.0"
+__version__ = "6.6.3"

From f292a911caccf9f52bb8dda7cd920ed1b6cdc738 Mon Sep 17 00:00:00 2001
From: Jody Phelan <jody.phelan@lshtm.ac.uk>
Date: Mon, 24 Feb 2025 16:10:47 +0000
Subject: [PATCH 2/5] add release template

---
 .github/release_template.md | 6 ++++++
 1 file changed, 6 insertions(+)
 create mode 100644 .github/release_template.md

diff --git a/.github/release_template.md b/.github/release_template.md
new file mode 100644
index 0000000..ff48170
--- /dev/null
+++ b/.github/release_template.md
@@ -0,0 +1,6 @@
+# Checks
+
+- [] Tests completed sucessfully
+- [] In code matches release version
+
+# Changes
\ No newline at end of file

From 410881685e2fe916c38761fa22982aa5ec522a3c Mon Sep 17 00:00:00 2001
From: Jody Phelan <jody.phelan@lshtm.ac.uk>
Date: Mon, 24 Feb 2025 16:23:28 +0000
Subject: [PATCH 3/5] remove template

---
 .github/release_template.md | 6 ------
 1 file changed, 6 deletions(-)
 delete mode 100644 .github/release_template.md

diff --git a/.github/release_template.md b/.github/release_template.md
deleted file mode 100644
index ff48170..0000000
--- a/.github/release_template.md
+++ /dev/null
@@ -1,6 +0,0 @@
-# Checks
-
-- [] Tests completed sucessfully
-- [] In code matches release version
-
-# Changes
\ No newline at end of file

From bf3a642311ad1edd1c47a6d1a35301732851b5cd Mon Sep 17 00:00:00 2001
From: Jody Phelan <jody.phelan@lshtm.ac.uk>
Date: Mon, 24 Feb 2025 16:35:07 +0000
Subject: [PATCH 4/5] update tests

---
 tests/run_test.py | 5 ++++-
 1 file changed, 4 insertions(+), 1 deletion(-)

diff --git a/tests/run_test.py b/tests/run_test.py
index 8c7a5dc..c7efdc6 100644
--- a/tests/run_test.py
+++ b/tests/run_test.py
@@ -71,8 +71,11 @@ def test_collate():
 
 def test_tbp_parser():
     run_cmd("git clone https://github.com/theiagen/tbp-parser.git")
+    os.mkdir("tbp-parser/tb-profiler-test")
+    os.chdir("tbp-parser/tb-profiler-test")
+
     run_cmd("samtools index bam/por5A_fastq.bam")
-    run_cmd('python tbp-parser/tbp_parser/tbp_parser.py results/por5A_freebayes.results.json bam/por5A_fastq.bam    -o "example-tbp-parser"    --min_depth 12     --min_frequency 0.9     --sequencing_method "Illumina NextSeq"    --operator "John Doe"')
+    run_cmd('python ../tbp_parser/tbp_parser.py ../../results/por5A_freebayes.results.json ../../bam/por5A_fastq.bam    -o "example-tbp-parser"    --min_depth 12     --min_frequency 0.9     --sequencing_method "Illumina NextSeq"    --operator "John Doe"')
     test_text = ','.join([l.strip().split(',')[:-2] for l in open("example-tbp-parser.looker_report.csv")][1])
     target_text = "por5A_freebayes,Illumina NextSeq,U,S-Interim,U,U,R,R,R,U,S,U,S,R,R,U,lineage4,DNA of Mycobacterium tuberculosis species detected"
     assert test_text == target_text
\ No newline at end of file

From ca1ff20ac48f3c4878b490117af07d49a32d1d5b Mon Sep 17 00:00:00 2001
From: Jody Phelan <jody.phelan@lshtm.ac.uk>
Date: Mon, 24 Feb 2025 16:55:44 +0000
Subject: [PATCH 5/5] update tests

---
 tests/run_test.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/tests/run_test.py b/tests/run_test.py
index c7efdc6..d5fcf9e 100644
--- a/tests/run_test.py
+++ b/tests/run_test.py
@@ -74,7 +74,7 @@ def test_tbp_parser():
     os.mkdir("tbp-parser/tb-profiler-test")
     os.chdir("tbp-parser/tb-profiler-test")
 
-    run_cmd("samtools index bam/por5A_fastq.bam")
+    run_cmd("samtools index ../../bam/por5A_fastq.bam")
     run_cmd('python ../tbp_parser/tbp_parser.py ../../results/por5A_freebayes.results.json ../../bam/por5A_fastq.bam    -o "example-tbp-parser"    --min_depth 12     --min_frequency 0.9     --sequencing_method "Illumina NextSeq"    --operator "John Doe"')
     test_text = ','.join([l.strip().split(',')[:-2] for l in open("example-tbp-parser.looker_report.csv")][1])
     target_text = "por5A_freebayes,Illumina NextSeq,U,S-Interim,U,U,R,R,R,U,S,U,S,R,R,U,lineage4,DNA of Mycobacterium tuberculosis species detected"