Merge branch 'release/v4.2.0'

ACEnglish · Jan 12, 2024 · bd39129 · bd39129
2 parents 1f32b66 + b304c0f
commit bd39129
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Showing 229 changed files with 9,792 additions and 7,650 deletions.
diff --git a/.github/workflows/codeql-analysis.yml b/.github/workflows/codeql-analysis.yml
@@ -38,7 +38,7 @@ jobs:
 
     # Initializes the CodeQL tools for scanning.
     - name: Initialize CodeQL
-      uses: github/codeql-action/init@v1
+      uses: github/codeql-action/init@v2
       with:
         languages: ${{ matrix.language }}
         # If you wish to specify custom queries, you can do so here or in a config file.
@@ -49,7 +49,7 @@ jobs:
     # Autobuild attempts to build any compiled languages  (C/C++, C#, or Java).
     # If this step fails, then you should remove it and run the build manually (see below)
     - name: Autobuild
-      uses: github/codeql-action/autobuild@v1
+      uses: github/codeql-action/autobuild@v2
 
     # ℹ️ Command-line programs to run using the OS shell.
     # 📚 https://git.io/JvXDl
@@ -63,4 +63,4 @@ jobs:
     #   make release
 
     - name: Perform CodeQL Analysis
-      uses: github/codeql-action/analyze@v1
+      uses: github/codeql-action/analyze@v2
diff --git a/.github/workflows/release.yml b/.github/workflows/release.yml
@@ -35,8 +35,8 @@ jobs:
           python -m pip install .
       - name: Build the release tarball
         run: |
-          python -m pip install --upgrade pip setuptools wheel
-          python setup.py sdist bdist_wheel
+          python -m pip install --upgrade pip setuptools wheel build
+          python3 -m build --wheel --sdist
       - name: Publish distribution 📦 to Test PyPI
         if: github.event.inputs.skip_test != 'skip'
         uses: pypa/gh-action-pypi-publish@master
@@ -47,7 +47,7 @@ jobs:
         uses: actions/upload-artifact@v2
         with:
           name: release-tarball
-          path: dist/Truvari*.tar.gz
+          path: dist/truvari*.tar.gz
           # if-no-files-found: ignore
       - name: Publish distribution 📦 to PyPI
         if: github.event.inputs.official == 'PUBLISH TO PYPI'

diff --git a/.pylintrc b/.pylintrc
@@ -28,7 +28,7 @@ unsafe-load-any-extension=no
 # A comma-separated list of package or module names from where C extensions may
 # be loaded. Extensions are loading into the active Python interpreter and may
 # run arbitrary code
-extension-pkg-whitelist=biograph._capi,tabix,pysam,intervaltree,edlib,setproctitle
+extension-pkg-whitelist=tabix,pysam,intervaltree,edlib,setproctitle,pyabpoa,pywfa
 
 
 [MESSAGES CONTROL]

diff --git a/Dockerfile b/Dockerfile
@@ -9,7 +9,9 @@ RUN apt-get -qq update \
   && \
   rm -rf /var/lib/apt/lists/*
 
-ADD . /opt/truvari-source
+RUN mkdir -p /opt/truvari-source/truvari/
+COPY setup.py README.md /opt/truvari-source
+COPY truvari/ /opt/truvari-source/truvari/
 WORKDIR /opt/truvari-source
 
 RUN wget https://mafft.cbrc.jp/alignment/software/mafft_7.505-1_amd64.deb \

diff --git a/LICENSE b/LICENSE
@@ -1,4 +1,4 @@
-Copyright 2021 Spiral Genetics
+Copyright 2024 Adam English
 
 Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated
 documentation files (the "Software"), to deal in the Software without restriction, including without limitation the

diff --git a/docs/requirements.txt b/docs/requirements.txt
@@ -2,11 +2,14 @@ pywfa>=0.5.1
 sphinx==4.2.0
 sphinx_rtd_theme==1.0.0
 readthedocs-sphinx-search==0.1.1
+pywfa>=0.5.1
+rich>=12.5.1
 edlib>=1.3.9
 pysam>=0.22
-intervaltree>=3.0.2
+intervaltree>=3.1
 joblib>=1.2.0
-numpy>=1.23.3
+numpy>=1.24.4
 pytabix>=0.1
 bwapy>=0.1.4
-pandas>=1.4.4
+pandas>=1.5.3
+pyabpoa>=1.4.3
diff --git a/imgs/coverage.svg b/imgs/coverage.svg
diff --git a/pyproject.toml b/pyproject.toml
@@ -0,0 +1,39 @@
+[build-system]
+requires = ["setuptools >= 69.0"]
+build-backend = "setuptools.build_meta"
+
+[project]
+name = "truvari"
+authors = [
+    {name = "ACEnglish", email="[email protected]"}
+]
+description = "Structural variant comparison tool for VCFs"
+readme = "README.md"
+license = { text = "MIT" }
+dynamic = ["version"]
+requires-python = ">=3.8"
+dependencies = [
+    "pywfa>=0.5.1",
+    "rich>=12.5.1",
+    "edlib>=1.3.9",
+    "pysam>=0.22",
+    "intervaltree>=3.1",
+    "joblib>=1.2.0",
+    "numpy>=1.24.4",
+    "pytabix>=0.1",
+    "bwapy>=0.1.4",
+    "pandas>=1.5.3",
+    "pyabpoa>=1.4.3",
+]
+
+[project.scripts]
+truvari = "truvari.__main__:main"
+
+[project.urls]
+Homepage = "https://github.com/ACEnglish/truvari"
+Documentation = "https://truvari.readthedocs.io/en/latest/"
+Issues = "https://github.com/ACEnglish/truvari/issues"
+Changelog = "https://github.com/ACEnglish/truvari/wiki/Updates"
+
+[tool.setuptools]
+packages = ["truvari", "truvari.annotations"]
diff --git a/repo_utils/answer_key/anno_answers.vcf.gz b/repo_utils/answer_key/anno_answers.vcf.gz
diff --git a/repo_utils/answer_key/anno_answers.vcf.gz.tbi b/repo_utils/answer_key/anno_answers.vcf.gz.tbi
diff --git a/repo_utils/answer_key/bench/bench12/candidate.refine.bed b/repo_utils/answer_key/bench/bench12/candidate.refine.bed
@@ -0,0 +1,9 @@
+chr20	258766	258767
+chr20	278929	279069
+chr20	380877	380878
+chr20	420664	420665
+chr20	641912	642330
+chr20	709758	709852
+chr20	727507	727556
+chr20	764536	764537
+chr20	949515	949619
diff --git a/repo_utils/answer_key/bench/bench12/fn.vcf.gz b/repo_utils/answer_key/bench/bench12/fn.vcf.gz
diff --git a/repo_utils/answer_key/bench/bench12/fn.vcf.gz.tbi b/repo_utils/answer_key/bench/bench12/fn.vcf.gz.tbi
diff --git a/repo_utils/answer_key/bench/bench12/fp.vcf.gz b/repo_utils/answer_key/bench/bench12/fp.vcf.gz
diff --git a/repo_utils/answer_key/bench/bench12/fp.vcf.gz.tbi b/repo_utils/answer_key/bench/bench12/fp.vcf.gz.tbi
diff --git a/repo_utils/answer_key/bench/bench12/log.txt b/repo_utils/answer_key/bench/bench12/log.txt
@@ -1,48 +1,47 @@
-2022-12-01 18:25:54,715 [INFO] Truvari v4.0.0.dev0+detached
-2022-12-01 18:25:54,716 [INFO] Command /data/truvari/__main__.py bench -b repo_utils/test_files/variants/input1.vcf.gz -c repo_utils/test_files/variants/input2.vcf.gz -f repo_utils/test_files/references/reference.fa -o test_results/bench12/
-2022-12-01 18:25:54,717 [INFO] Params:
+2024-01-09 03:54:51,643 [INFO] Truvari v4.2.0rc1
+2024-01-09 03:54:51,645 [INFO] Command /data/truvari/__main__.py bench -b repo_utils/test_files/variants/input1.vcf.gz -c repo_utils/test_files/variants/input2.vcf.gz -f repo_utils/test_files/references/reference.fa -o test_results/bench12/
+2024-01-09 03:54:51,646 [INFO] Params:
 {
     "base": "/data/repo_utils/test_files/variants/input1.vcf.gz",
     "comp": "/data/repo_utils/test_files/variants/input2.vcf.gz",
     "output": "test_results/bench12/",
-    "reference": "/data/repo_utils/test_files/references/reference.fa",
+    "includebed": null,
+    "extend": 0,
     "debug": false,
-    "prog": false,
+    "reference": "/data/repo_utils/test_files/references/reference.fa",
     "refdist": 500,
-    "pctsim": 0.7,
+    "pctseq": 0.7,
     "minhaplen": 50,
     "pctsize": 0.7,
     "pctovl": 0.0,
     "typeignore": false,
-    "dup_to_ins": false,
-    "use_lev": false,
     "chunksize": 1000,
-    "gtcomp": false,
     "bSample": "NA24385",
     "cSample": "NA12878",
+    "dup_to_ins": false,
     "sizemin": 50,
     "sizefilt": 30,
     "sizemax": 50000,
     "passonly": false,
     "no_ref": false,
-    "includebed": null,
-    "extend": 0,
-    "multimatch": false
+    "pick": "single",
+    "check_monref": true,
+    "check_multi": true
 }
-2022-12-01 18:25:54,891 [INFO] Zipped 3934 variants Counter({'base': 2151, 'comp': 1783})
-2022-12-01 18:25:54,892 [INFO] 13 chunks of 3934 variants Counter({'__filtered': 3904, 'base': 16, 'comp': 14})
-2022-12-01 18:25:54,897 [INFO] Stats: {
+2024-01-09 03:54:51,858 [INFO] Zipped 3934 variants Counter({'base': 2151, 'comp': 1783})
+2024-01-09 03:54:51,868 [INFO] 13 chunks of 3934 variants Counter({'__filtered': 3904, 'base': 16, 'comp': 14})
+2024-01-09 03:54:51,993 [INFO] Stats: {
     "TP-base": 8,
-    "TP-call": 8,
+    "TP-comp": 8,
     "FP": 3,
     "FN": 8,
     "precision": 0.7272727272727273,
     "recall": 0.5,
     "f1": 0.5925925925925926,
     "base cnt": 16,
-    "call cnt": 11,
-    "TP-call_TP-gt": 4,
-    "TP-call_FP-gt": 4,
+    "comp cnt": 11,
+    "TP-comp_TP-gt": 4,
+    "TP-comp_FP-gt": 4,
     "TP-base_TP-gt": 4,
     "TP-base_FP-gt": 4,
     "gt_concordance": 0.5,
@@ -60,6 +59,26 @@
         "(1, 0)": {
             "(1, 1)": 1
         }
+    },
+    "weighted": {
+        "sequence": {
+            "TP": 12.533399924635887,
+            "FP": 1.6414000391960144,
+            "FN": 4.268600061535835,
+            "precision": 0.8842029486564768,
+            "recall": 0.7459469072105135,
+            "f1": 0.8092120519139951,
+            "total": 18
+        },
+        "size": {
+            "TP": 10.914199993014336,
+            "FP": 2.0859000086784363,
+            "FN": 5.752500012516975,
+            "precision": 0.8395473874503406,
+            "recall": 0.6548506896621499,
+            "f1": 0.7357854564939021,
+            "total": 18
+        }
     }
 }
-2022-12-01 18:25:54,987 [INFO] Finished bench
+2024-01-09 03:54:51,994 [INFO] Finished bench
diff --git a/repo_utils/answer_key/bench/bench12/params.json b/repo_utils/answer_key/bench/bench12/params.json
@@ -1 +1 @@
-{"base": "/data/repo_utils/test_files/variants/input1.vcf.gz", "comp": "/data/repo_utils/test_files/variants/input2.vcf.gz", "output": "test_results/bench12/", "reference": "/data/repo_utils/test_files/references/reference.fa", "debug": false, "prog": false, "refdist": 500, "pctsim": 0.7, "minhaplen": 50, "pctsize": 0.7, "pctovl": 0.0, "typeignore": false, "dup_to_ins": false, "use_lev": false, "chunksize": 1000, "gtcomp": false, "bSample": "NA24385", "cSample": "NA12878", "sizemin": 50, "sizefilt": 30, "sizemax": 50000, "passonly": false, "no_ref": false, "includebed": null, "extend": 0, "multimatch": false}
+{"base": "/data/repo_utils/test_files/variants/input1.vcf.gz", "comp": "/data/repo_utils/test_files/variants/input2.vcf.gz", "output": "test_results/bench12/", "includebed": null, "extend": 0, "debug": false, "reference": "/data/repo_utils/test_files/references/reference.fa", "refdist": 500, "pctseq": 0.7, "minhaplen": 50, "pctsize": 0.7, "pctovl": 0.0, "typeignore": false, "chunksize": 1000, "bSample": "NA24385", "cSample": "NA12878", "dup_to_ins": false, "sizemin": 50, "sizefilt": 30, "sizemax": 50000, "passonly": false, "no_ref": false, "pick": "single", "check_monref": true, "check_multi": true}
diff --git a/repo_utils/answer_key/bench/bench12/summary.json b/repo_utils/answer_key/bench/bench12/summary.json
@@ -28,4 +28,4 @@
             "(1, 1)": 1
         }
     }
-}
+}
diff --git a/repo_utils/answer_key/bench/bench12/tp-base.vcf.gz b/repo_utils/answer_key/bench/bench12/tp-base.vcf.gz
diff --git a/repo_utils/answer_key/bench/bench12/tp-base.vcf.gz.tbi b/repo_utils/answer_key/bench/bench12/tp-base.vcf.gz.tbi
diff --git a/repo_utils/answer_key/bench/bench12/tp-comp.vcf.gz b/repo_utils/answer_key/bench/bench12/tp-comp.vcf.gz
diff --git a/repo_utils/answer_key/bench/bench12/tp-comp.vcf.gz.tbi b/repo_utils/answer_key/bench/bench12/tp-comp.vcf.gz.tbi
diff --git a/repo_utils/answer_key/bench/bench12_gtcomp/candidate.refine.bed b/repo_utils/answer_key/bench/bench12_gtcomp/candidate.refine.bed
@@ -0,0 +1,8 @@
+chr20	258766	258767
+chr20	278929	279069
+chr20	380877	380878
+chr20	641912	642330
+chr20	709758	709852
+chr20	727507	727556
+chr20	764536	764537
+chr20	949515	949619
diff --git a/repo_utils/answer_key/bench/bench12_gtcomp/fn.vcf.gz b/repo_utils/answer_key/bench/bench12_gtcomp/fn.vcf.gz
diff --git a/repo_utils/answer_key/bench/bench12_gtcomp/fn.vcf.gz.tbi b/repo_utils/answer_key/bench/bench12_gtcomp/fn.vcf.gz.tbi
diff --git a/repo_utils/answer_key/bench/bench12_gtcomp/fp.vcf.gz b/repo_utils/answer_key/bench/bench12_gtcomp/fp.vcf.gz
diff --git a/repo_utils/answer_key/bench/bench12_gtcomp/fp.vcf.gz.tbi b/repo_utils/answer_key/bench/bench12_gtcomp/fp.vcf.gz.tbi
diff --git a/repo_utils/answer_key/bench/bench12_gtcomp/log.txt b/repo_utils/answer_key/bench/bench12_gtcomp/log.txt
@@ -1,48 +1,47 @@
-2022-12-01 18:26:08,784 [INFO] Truvari v4.0.0.dev0+detached
-2022-12-01 18:26:08,785 [INFO] Command /data/truvari/__main__.py bench -b repo_utils/test_files/variants/input1.vcf.gz -c repo_utils/test_files/variants/input2.vcf.gz -f repo_utils/test_files/references/reference.fa -o test_results/bench12_gtcomp/ --gtcomp
-2022-12-01 18:26:08,786 [INFO] Params:
+2024-01-09 03:55:04,513 [INFO] Truvari v4.2.0rc1
+2024-01-09 03:55:04,514 [INFO] Command /data/truvari/__main__.py bench -b repo_utils/test_files/variants/input1.vcf.gz -c repo_utils/test_files/variants/input2.vcf.gz -f repo_utils/test_files/references/reference.fa -o test_results/bench12_gtcomp/ --pick ac
+2024-01-09 03:55:04,515 [INFO] Params:
 {
     "base": "/data/repo_utils/test_files/variants/input1.vcf.gz",
     "comp": "/data/repo_utils/test_files/variants/input2.vcf.gz",
     "output": "test_results/bench12_gtcomp/",
-    "reference": "/data/repo_utils/test_files/references/reference.fa",
+    "includebed": null,
+    "extend": 0,
     "debug": false,
-    "prog": false,
+    "reference": "/data/repo_utils/test_files/references/reference.fa",
     "refdist": 500,
-    "pctsim": 0.7,
+    "pctseq": 0.7,
     "minhaplen": 50,
     "pctsize": 0.7,
     "pctovl": 0.0,
     "typeignore": false,
-    "dup_to_ins": false,
-    "use_lev": false,
     "chunksize": 1000,
-    "gtcomp": true,
     "bSample": "NA24385",
     "cSample": "NA12878",
+    "dup_to_ins": false,
     "sizemin": 50,
     "sizefilt": 30,
     "sizemax": 50000,
     "passonly": false,
     "no_ref": false,
-    "includebed": null,
-    "extend": 0,
-    "multimatch": false
+    "pick": "ac",
+    "check_monref": true,
+    "check_multi": true
 }
-2022-12-01 18:26:08,975 [INFO] Zipped 3934 variants Counter({'base': 2151, 'comp': 1783})
-2022-12-01 18:26:08,976 [INFO] 13 chunks of 3934 variants Counter({'__filtered': 3904, 'base': 16, 'comp': 14})
-2022-12-01 18:26:08,981 [INFO] Stats: {
+2024-01-09 03:55:04,725 [INFO] Zipped 3934 variants Counter({'base': 2151, 'comp': 1783})
+2024-01-09 03:55:04,726 [INFO] 13 chunks of 3934 variants Counter({'__filtered': 3904, 'base': 16, 'comp': 14})
+2024-01-09 03:55:04,843 [INFO] Stats: {
     "TP-base": 9,
-    "TP-call": 8,
+    "TP-comp": 8,
     "FP": 3,
     "FN": 7,
     "precision": 0.7272727272727273,
     "recall": 0.5625,
     "f1": 0.6343612334801763,
     "base cnt": 16,
-    "call cnt": 11,
-    "TP-call_TP-gt": 4,
-    "TP-call_FP-gt": 4,
+    "comp cnt": 11,
+    "TP-comp_TP-gt": 4,
+    "TP-comp_FP-gt": 4,
     "TP-base_TP-gt": 4,
     "TP-base_FP-gt": 5,
     "gt_concordance": 0.5,
@@ -60,6 +59,26 @@
         "(1, 0)": {
             "(1, 1)": 1
         }
+    },
+    "weighted": {
+        "sequence": {
+            "TP": 12.533399924635887,
+            "FP": 1.6414000391960144,
+            "FN": 4.268600061535835,
+            "precision": 0.8842029486564768,
+            "recall": 0.7459469072105135,
+            "f1": 0.8092120519139951,
+            "total": 18
+        },
+        "size": {
+            "TP": 10.914199993014336,
+            "FP": 2.0859000086784363,
+            "FN": 5.752500012516975,
+            "precision": 0.8395473874503406,
+            "recall": 0.6548506896621499,
+            "f1": 0.7357854564939021,
+            "total": 18
+        }
     }
 }
-2022-12-01 18:26:09,088 [INFO] Finished bench
+2024-01-09 03:55:04,844 [INFO] Finished bench
diff --git a/repo_utils/answer_key/bench/bench12_gtcomp/params.json b/repo_utils/answer_key/bench/bench12_gtcomp/params.json
@@ -1 +1 @@
-{"base": "/data/repo_utils/test_files/variants/input1.vcf.gz", "comp": "/data/repo_utils/test_files/variants/input2.vcf.gz", "output": "test_results/bench12_gtcomp/", "reference": "/data/repo_utils/test_files/references/reference.fa", "debug": false, "prog": false, "refdist": 500, "pctsim": 0.7, "minhaplen": 50, "pctsize": 0.7, "pctovl": 0.0, "typeignore": false, "dup_to_ins": false, "use_lev": false, "chunksize": 1000, "gtcomp": true, "bSample": "NA24385", "cSample": "NA12878", "sizemin": 50, "sizefilt": 30, "sizemax": 50000, "passonly": false, "no_ref": false, "includebed": null, "extend": 0, "multimatch": false}
+{"base": "/data/repo_utils/test_files/variants/input1.vcf.gz", "comp": "/data/repo_utils/test_files/variants/input2.vcf.gz", "output": "test_results/bench12_gtcomp/", "includebed": null, "extend": 0, "debug": false, "reference": "/data/repo_utils/test_files/references/reference.fa", "refdist": 500, "pctseq": 0.7, "minhaplen": 50, "pctsize": 0.7, "pctovl": 0.0, "typeignore": false, "chunksize": 1000, "bSample": "NA24385", "cSample": "NA12878", "dup_to_ins": false, "sizemin": 50, "sizefilt": 30, "sizemax": 50000, "passonly": false, "no_ref": false, "pick": "ac", "check_monref": true, "check_multi": true}
diff --git a/repo_utils/answer_key/bench/bench12_gtcomp/summary.json b/repo_utils/answer_key/bench/bench12_gtcomp/summary.json
@@ -28,4 +28,4 @@
             "(1, 1)": 1
         }
     }
-}
+}
diff --git a/repo_utils/answer_key/bench/bench12_gtcomp/tp-base.vcf.gz b/repo_utils/answer_key/bench/bench12_gtcomp/tp-base.vcf.gz
diff --git a/repo_utils/answer_key/bench/bench12_gtcomp/tp-base.vcf.gz.tbi b/repo_utils/answer_key/bench/bench12_gtcomp/tp-base.vcf.gz.tbi
diff --git a/repo_utils/answer_key/bench/bench12_gtcomp/tp-comp.vcf.gz b/repo_utils/answer_key/bench/bench12_gtcomp/tp-comp.vcf.gz
diff --git a/repo_utils/answer_key/bench/bench12_gtcomp/tp-comp.vcf.gz.tbi b/repo_utils/answer_key/bench/bench12_gtcomp/tp-comp.vcf.gz.tbi
diff --git a/repo_utils/answer_key/bench/bench13/candidate.refine.bed b/repo_utils/answer_key/bench/bench13/candidate.refine.bed
@@ -0,0 +1,10 @@
+chr20	149012	149073
+chr20	183616	183617
+chr20	258766	258767
+chr20	280210	280275
+chr20	380877	380911
+chr20	420664	420665
+chr20	641905	642391
+chr20	709758	709852
+chr20	727555	727590
+chr20	764441	764537
diff --git a/repo_utils/answer_key/bench/bench13/fn.vcf.gz b/repo_utils/answer_key/bench/bench13/fn.vcf.gz
diff --git a/repo_utils/answer_key/bench/bench13/fn.vcf.gz.tbi b/repo_utils/answer_key/bench/bench13/fn.vcf.gz.tbi
diff --git a/repo_utils/answer_key/bench/bench13/fp.vcf.gz b/repo_utils/answer_key/bench/bench13/fp.vcf.gz
diff --git a/repo_utils/answer_key/bench/bench13/fp.vcf.gz.tbi b/repo_utils/answer_key/bench/bench13/fp.vcf.gz.tbi
Original file line number	Diff line number	Diff line change
		@@ -1 +1 @@
		{"base": "/data/repo_utils/test_files/variants/input1.vcf.gz", "comp": "/data/repo_utils/test_files/variants/input2.vcf.gz", "output": "test_results/bench12/", "reference": "/data/repo_utils/test_files/references/reference.fa", "debug": false, "prog": false, "refdist": 500, "pctsim": 0.7, "minhaplen": 50, "pctsize": 0.7, "pctovl": 0.0, "typeignore": false, "dup_to_ins": false, "use_lev": false, "chunksize": 1000, "gtcomp": false, "bSample": "NA24385", "cSample": "NA12878", "sizemin": 50, "sizefilt": 30, "sizemax": 50000, "passonly": false, "no_ref": false, "includebed": null, "extend": 0, "multimatch": false}
		{"base": "/data/repo_utils/test_files/variants/input1.vcf.gz", "comp": "/data/repo_utils/test_files/variants/input2.vcf.gz", "output": "test_results/bench12/", "includebed": null, "extend": 0, "debug": false, "reference": "/data/repo_utils/test_files/references/reference.fa", "refdist": 500, "pctseq": 0.7, "minhaplen": 50, "pctsize": 0.7, "pctovl": 0.0, "typeignore": false, "chunksize": 1000, "bSample": "NA24385", "cSample": "NA12878", "dup_to_ins": false, "sizemin": 50, "sizefilt": 30, "sizemax": 50000, "passonly": false, "no_ref": false, "pick": "single", "check_monref": true, "check_multi": true}
-Original file line number
+Diff line change
@@ Expand Up / @@ -28,4 +28,4 @@ @@
                 "(1, 1)": 1
             }
         }
-    }
+    }