bio-grumpy 0.2.7__tar.gz → 1.0.0__tar.gz

{bio_grumpy-0.2.7 → bio_grumpy-1.0.0}/.gitignore

@@ -14,6 +14,7 @@ Cargo.lock
 *.pdb
 
 massif.out.*
+mprofile*
 perf.data*
 tarpaulin-*.html
 edge-cases.md

{bio_grumpy-0.2.7 → bio_grumpy-1.0.0}/Cargo.lock

@@ -96,7 +96,7 @@ dependencies = [
 
 [[package]]
 name = "grumpy"
-version = "0.2.7"
+version = "1.0.0"
 dependencies = [
  "gb-io",
  "ordered-float",
@@ -136,9 +136,9 @@ checksum = "d750af042f7ef4f724306de029d18836c26c1765a54a6a3f094cbd23a7267ffa"
 
 [[package]]
 name = "lock_api"
-version = "0.4.12"
+version = "0.4.13"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "07af8b9cdd281b7915f413fa73f29ebd5d55d0d3f0155584dade1ff18cea1b17"
+checksum = "96936507f153605bddfcda068dd804796c84324ed2510809e5b2a624c81da765"
 dependencies = [
  "autocfg",
  "scopeguard",
@@ -223,9 +223,9 @@ dependencies = [
 
 [[package]]
 name = "parking_lot"
-version = "0.12.3"
+version = "0.12.4"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "f1bf18183cf54e8d6059647fc3063646a1801cf30896933ec2311622cc4b9a27"
+checksum = "70d58bf43669b5795d1576d0641cfb6fbb2057bf629506267a92807158584a13"
 dependencies = [
  "lock_api",
  "parking_lot_core",
@@ -233,9 +233,9 @@ dependencies = [
 
 [[package]]
 name = "parking_lot_core"
-version = "0.9.10"
+version = "0.9.11"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "1e401f977ab385c9e4e3ab30627d6f26d00e2c73eef317493c4ec6d468726cf8"
+checksum = "bc838d2a56b5b1a6c25f55575dfc605fabb63bb2365f6c2353ef9159aa69e4a5"
 dependencies = [
  "cfg-if",
  "libc",

{bio_grumpy-0.2.7 → bio_grumpy-1.0.0}/Cargo.toml

@@ -1,6 +1,6 @@
 [package]
 name = "grumpy"
-version = "0.2.7"
+version = "1.0.0"
 edition = "2021"
 description = "Genetic analysis in Rust."
 license-file = "LICENSE"

{bio_grumpy-0.2.7 → bio_grumpy-1.0.0}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: bio-grumpy
-Version: 0.2.7
+Version: 1.0.0
 Classifier: Development Status :: 5 - Production/Stable
 Classifier: Programming Language :: Rust
 Classifier: Programming Language :: Python :: Implementation :: CPython

{bio_grumpy-0.2.7 → bio_grumpy-1.0.0}/src/common.rs

@@ -51,6 +51,12 @@ pub struct VCFRow {
     #[pyo3(get, set)]
     /// True if the filter column passes
     pub is_filter_pass: bool,
+
+    #[pyo3(get, set)]
+    /// Whether this VCF row is complex
+    /// Complex VCF rows are edge cases where a row has a large (>1,000) bases for the ref as well as >1 alt
+    /// This is used to flag when mutations' evidence isn't worth fetching due to size.
+    pub is_complex: bool,
 }
 
 #[pyclass(eq)]

{bio_grumpy-0.2.7 → bio_grumpy-1.0.0}/src/genome.rs

@@ -861,6 +861,7 @@ mod tests {
                     ("GT_CONF".to_string(), vec!["613.77".to_string()]),
                 ]),
                 is_filter_pass: true,
+                is_complex: false,
             },
             VCFRow {
                 // 1
@@ -875,6 +876,7 @@ mod tests {
                     ("GT_CONF".to_string(), vec!["613.77".to_string()]),
                 ]),
                 is_filter_pass: false,
+                is_complex: false,
             },
             VCFRow {
                 // 2
@@ -892,6 +894,7 @@ mod tests {
                     ("GT_CONF".to_string(), vec!["613.77".to_string()]),
                 ]),
                 is_filter_pass: true,
+                is_complex: false,
             },
             VCFRow {
                 // 3
@@ -906,6 +909,7 @@ mod tests {
                     ("GT_CONF".to_string(), vec!["63.77".to_string()]),
                 ]),
                 is_filter_pass: true,
+                is_complex: false,
             },
             VCFRow {
                 // 4
@@ -920,6 +924,7 @@ mod tests {
                     ("GT_CONF".to_string(), vec!["63.77".to_string()]),
                 ]),
                 is_filter_pass: false,
+                is_complex: false,
             },
             VCFRow {
                 // 5
@@ -934,6 +939,7 @@ mod tests {
                     ("GT_CONF".to_string(), vec!["613.77".to_string()]),
                 ]),
                 is_filter_pass: false,
+                is_complex: false,
             },
             VCFRow {
                 // 6
@@ -948,6 +954,7 @@ mod tests {
                     ("GT_CONF".to_string(), vec!["613.77".to_string()]),
                 ]),
                 is_filter_pass: true,
+                is_complex: false,
             },
             VCFRow {
                 // 7
@@ -962,6 +969,7 @@ mod tests {
                     ("GT_CONF".to_string(), vec!["613.77".to_string()]),
                 ]),
                 is_filter_pass: true,
+                is_complex: false,
             },
             VCFRow {
                 // 8
@@ -980,6 +988,7 @@ mod tests {
                     ("GT_CONF".to_string(), vec!["613".to_string()]),
                 ]),
                 is_filter_pass: false,
+                is_complex: false,
             },
             VCFRow {
                 // 9
@@ -998,6 +1007,7 @@ mod tests {
                     ("GT_CONF".to_string(), vec!["3.77".to_string()]),
                 ]),
                 is_filter_pass: false,
+                is_complex: false,
             },
             VCFRow {
                 // 10
@@ -1014,6 +1024,7 @@ mod tests {
                     ("GT_CONF".to_string(), vec!["613".to_string()]),
                 ]),
                 is_filter_pass: false,
+                is_complex: false,
             },
             VCFRow {
                 // 11
@@ -1029,6 +1040,7 @@ mod tests {
                     ("GT_CONF".to_string(), vec!["613".to_string()]),
                 ]),
                 is_filter_pass: false,
+                is_complex: false,
             },
         ];
 
@@ -1456,6 +1468,7 @@ mod tests {
                     ("GT_CONF".to_string(), vec!["2.05".to_string()]),
                 ]),
                 is_filter_pass: true,
+                is_complex: false,
             },
             VCFRow {
                 // 1
@@ -1477,6 +1490,7 @@ mod tests {
                     ("GT_CONF".to_string(), vec!["3.77".to_string()]),
                 ]),
                 is_filter_pass: false,
+                is_complex: false,
             },
             VCFRow {
                 // 2
@@ -1499,6 +1513,7 @@ mod tests {
                     ("GT_CONF".to_string(), vec!["2.76".to_string()]),
                 ]),
                 is_filter_pass: true,
+                is_complex: false,
             },
             VCFRow {
                 // 3
@@ -1513,6 +1528,7 @@ mod tests {
                     ("GT_CONF".to_string(), vec!["200.58".to_string()]),
                 ]),
                 is_filter_pass: true,
+                is_complex: false,
             },
             VCFRow {
                 // 4
@@ -1530,6 +1546,7 @@ mod tests {
                     ("GT_CONF".to_string(), vec!["155.58".to_string()]),
                 ]),
                 is_filter_pass: true,
+                is_complex: false,
             },
             VCFRow {
                 // 5
@@ -1547,6 +1564,7 @@ mod tests {
                     ("GT_CONF".to_string(), vec!["300.25".to_string()]),
                 ]),
                 is_filter_pass: true,
+                is_complex: false,
             },
             VCFRow {
                 // 6
@@ -1569,6 +1587,7 @@ mod tests {
                     ("GT_CONF".to_string(), vec!["613.77".to_string()]),
                 ]),
                 is_filter_pass: true,
+                is_complex: false,
             },
             VCFRow {
                 // 7
@@ -1591,6 +1610,7 @@ mod tests {
                     ("GT_CONF".to_string(), vec!["613.77".to_string()]),
                 ]),
                 is_filter_pass: true,
+                is_complex: false,
             },
             VCFRow {
                 // 8
@@ -1613,6 +1633,7 @@ mod tests {
                     ("GT_CONF".to_string(), vec!["475.54".to_string()]),
                 ]),
                 is_filter_pass: true,
+                is_complex: false,
             },
             VCFRow {
                 // 9
@@ -1635,6 +1656,7 @@ mod tests {
                     ("GT_CONF".to_string(), vec!["315.11".to_string()]),
                 ]),
                 is_filter_pass: true,
+                is_complex: false,
             },
             VCFRow {
                 // 10
@@ -1649,6 +1671,7 @@ mod tests {
                     ("GT_CONF".to_string(), vec!["145.21".to_string()]),
                 ]),
                 is_filter_pass: true,
+                is_complex: false,
             },
             VCFRow {
                 // 11
@@ -1663,6 +1686,7 @@ mod tests {
                     ("GT_CONF".to_string(), vec!["145.21".to_string()]),
                 ]),
                 is_filter_pass: true,
+                is_complex: false,
             },
             VCFRow {
                 // 12
@@ -1677,6 +1701,7 @@ mod tests {
                     ("GT_CONF".to_string(), vec!["145.21".to_string()]),
                 ]),
                 is_filter_pass: true,
+                is_complex: false,
             },
             VCFRow {
                 // 13
@@ -1691,6 +1716,7 @@ mod tests {
                     ("GT_CONF".to_string(), vec!["145.21".to_string()]),
                 ]),
                 is_filter_pass: true,
+                is_complex: false,
             },
             VCFRow {
                 // 14
@@ -1705,6 +1731,7 @@ mod tests {
                     ("GT_CONF".to_string(), vec!["145.21".to_string()]),
                 ]),
                 is_filter_pass: true,
+                is_complex: false,
             },
             VCFRow {
                 // 15
@@ -1722,6 +1749,7 @@ mod tests {
                     ("GT_CONF".to_string(), vec!["145.21".to_string()]),
                 ]),
                 is_filter_pass: true,
+                is_complex: false,
             },
         ];
 
@@ -3444,7 +3472,7 @@ mod tests {
                     ("COV".to_string(), vec!["1".to_string(), "3".to_string()]),
                     ("GT_CONF".to_string(), vec!["2.05".to_string()]),
                 ]),
-                is_filter_pass: true,
+                is_filter_pass: true, is_complex: false,
             }
         ];
 
@@ -3670,7 +3698,7 @@ mod tests {
                     ("COV".to_string(), vec!["1".to_string(), "3".to_string()]),
                     ("GT_CONF".to_string(), vec!["2.05".to_string()]),
                 ]),
-                is_filter_pass: true,
+                is_filter_pass: true, is_complex: false,
             }
 
         ];
@@ -3969,6 +3997,7 @@ mod tests {
                     ("GT_CONF_PERCENTILE".to_string(), vec!["77.89".to_string()]),
                 ]),
                 is_filter_pass: false,
+                is_complex: false,
             },
             VCFRow {
                 // 1
@@ -3990,6 +4019,7 @@ mod tests {
                     ("GT_CONF_PERCENTILE".to_string(), vec!["77.89".to_string()]),
                 ]),
                 is_filter_pass: false,
+                is_complex: false,
             },
         ];
 
@@ -4117,6 +4147,7 @@ mod tests {
                     ("GT_CONF_PERCENTILE".to_string(), vec!["77.89".to_string()]),
                 ]),
                 is_filter_pass: false,
+                is_complex: false,
             },
             VCFRow {
                 // 1
@@ -4139,6 +4170,7 @@ mod tests {
                     ("GT_CONF_PERCENTILE".to_string(), vec!["77.89".to_string()]),
                 ]),
                 is_filter_pass: false,
+                is_complex: false,
             },
         ];
 
@@ -4257,6 +4289,7 @@ mod tests {
                     ("GT_CONF_PERCENTILE".to_string(), vec!["77.89".to_string()]),
                 ]),
                 is_filter_pass: false,
+                is_complex: false,
             },
             VCFRow {
                 // 1
@@ -4278,6 +4311,7 @@ mod tests {
                     ("GT_CONF_PERCENTILE".to_string(), vec!["77.89".to_string()]),
                 ]),
                 is_filter_pass: false,
+                is_complex: false,
             },
         ];
 
@@ -4483,6 +4517,7 @@ mod tests {
                     ("GT_CONF".to_string(), vec!["2.05".to_string()]),
                 ]),
                 is_filter_pass: true,
+                is_complex: false,
             },
             VCFRow {
                 // 1
@@ -4497,6 +4532,7 @@ mod tests {
                     ("GT_CONF".to_string(), vec!["2.05".to_string()]),
                 ]),
                 is_filter_pass: true,
+                is_complex: false,
             },
             VCFRow {
                 // 2
@@ -4511,6 +4547,7 @@ mod tests {
                     ("GT_CONF".to_string(), vec!["2.05".to_string()]),
                 ]),
                 is_filter_pass: true,
+                is_complex: false,
             },
         ];
 

{bio_grumpy-0.2.7 → bio_grumpy-1.0.0}/src/vcf.rs

@@ -266,6 +266,8 @@ impl VCFFile {
             passed = true;
         }
 
+        let is_complex = record.reference.len() > 1000 && alts.len() > 1;
+
         let row = VCFRow {
             position: record.position as i64,
             reference: String::from_utf8_lossy(&record.reference)
@@ -275,6 +277,7 @@ impl VCFFile {
             filter: filters.clone(),
             fields: fields.clone(),
             is_filter_pass: passed,
+            is_complex,
         };
 
         let (record_calls, record_minor_calls) =
@@ -831,6 +834,7 @@ mod tests {
                     ("COV".to_string(), vec!["1".to_string()]),
                 ]),
                 is_filter_pass: true,
+                is_complex: false,
             };
             let (calls, minor_calls) = VCFFile::parse_record_for_calls(record, 1, 0);
             assert_eq!(calls.len(), 1);
@@ -858,6 +862,7 @@ mod tests {
                     ("COV".to_string(), vec!["1".to_string(), "2".to_string()]),
                 ]),
                 is_filter_pass: true,
+                is_complex: false,
             };
             let (calls, minor_calls) = VCFFile::parse_record_for_calls(record, 1, 0);
             assert_eq!(calls.len(), 1);
@@ -885,6 +890,7 @@ mod tests {
                     ("COV".to_string(), vec!["1".to_string(), "3".to_string()]),
                 ]),
                 is_filter_pass: true,
+                is_complex: false,
             };
             let (calls, minor_calls) = VCFFile::parse_record_for_calls(record, 2, 0);
             assert_eq!(calls.len(), 1);
@@ -924,6 +930,7 @@ mod tests {
                     ("COV".to_string(), vec!["1".to_string()]),
                 ]),
                 is_filter_pass: true,
+                is_complex: false,
             };
             let (calls, minor_calls) = VCFFile::parse_record_for_calls(record, 2, 0);
             assert_eq!(calls.len(), 1);
@@ -951,6 +958,7 @@ mod tests {
                     ("COV".to_string(), vec!["1".to_string()]),
                 ]),
                 is_filter_pass: true,
+                is_complex: false,
             };
             let (calls, minor_calls) = VCFFile::parse_record_for_calls(record, 1, 0);
             assert_eq!(calls.len(), 1);
@@ -978,6 +986,7 @@ mod tests {
                     ("COV".to_string(), vec!["1".to_string()]),
                 ]),
                 is_filter_pass: false,
+                is_complex: false,
             };
             let (calls, minor_calls) = VCFFile::parse_record_for_calls(record, 2, 0);
             assert_eq!(calls.len(), 1);
@@ -1005,6 +1014,7 @@ mod tests {
                     ("COV".to_string(), vec!["1".to_string(), "5".to_string()]),
                 ]),
                 is_filter_pass: true,
+                is_complex: false,
             };
             let (calls, minor_calls) = VCFFile::parse_record_for_calls(record, 3, 123);
             assert_eq!(calls.len(), 1);
@@ -1032,6 +1042,7 @@ mod tests {
                     ("COV".to_string(), vec!["1".to_string(), "5".to_string()]),
                 ]),
                 is_filter_pass: true,
+                is_complex: false,
             };
             let (calls, minor_calls) = VCFFile::parse_record_for_calls(record, 3, 0);
             assert_eq!(calls.len(), 1);
@@ -1059,6 +1070,7 @@ mod tests {
                     ("COV".to_string(), vec!["1".to_string(), "5".to_string()]),
                 ]),
                 is_filter_pass: true,
+                is_complex: false,
             };
             let (calls, minor_calls) = VCFFile::parse_record_for_calls(record, 3, 0);
             assert_eq!(calls.len(), 2);
@@ -1098,6 +1110,7 @@ mod tests {
                     ),
                 ]),
                 is_filter_pass: true,
+                is_complex: false,
             };
             let (calls, minor_calls) = VCFFile::parse_record_for_calls(record, 3, 0);
             assert_eq!(calls.len(), 2);
@@ -1180,6 +1193,7 @@ mod tests {
                     ("GT_CONF".to_string(), vec!["613.77".to_string()]),
                 ]),
                 is_filter_pass: true,
+                is_complex: false,
             },
             VCFRow {
                 position: 4725,
@@ -1193,6 +1207,7 @@ mod tests {
                     ("GT_CONF".to_string(), vec!["613.77".to_string()]),
                 ]),
                 is_filter_pass: false,
+                is_complex: false,
             },
             VCFRow {
                 position: 4730,
@@ -1209,6 +1224,7 @@ mod tests {
                     ("GT_CONF".to_string(), vec!["613.77".to_string()]),
                 ]),
                 is_filter_pass: true,
+                is_complex: false,
             },
             VCFRow {
                 position: 4735,
@@ -1222,6 +1238,7 @@ mod tests {
                     ("GT_CONF".to_string(), vec!["63.77".to_string()]),
                 ]),
                 is_filter_pass: true,
+                is_complex: false,
             },
             VCFRow {
                 position: 4740,
@@ -1235,6 +1252,7 @@ mod tests {
                     ("GT_CONF".to_string(), vec!["63.77".to_string()]),
                 ]),
                 is_filter_pass: false,
+                is_complex: false,
             },
             VCFRow {
                 position: 13148,
@@ -1248,6 +1266,7 @@ mod tests {
                     ("GT_CONF".to_string(), vec!["613.77".to_string()]),
                 ]),
                 is_filter_pass: false,
+                is_complex: false,
             },
             VCFRow {
                 position: 13149,
@@ -1261,6 +1280,7 @@ mod tests {
                     ("GT_CONF".to_string(), vec!["613.77".to_string()]),
                 ]),
                 is_filter_pass: true,
+                is_complex: false,
             },
             VCFRow {
                 position: 13150,
@@ -1274,6 +1294,7 @@ mod tests {
                     ("GT_CONF".to_string(), vec!["613.77".to_string()]),
                 ]),
                 is_filter_pass: true,
+                is_complex: false,
             },
             VCFRow {
                 position: 13333,
@@ -1290,6 +1311,7 @@ mod tests {
                     ("GT_CONF".to_string(), vec!["613".to_string()]),
                 ]),
                 is_filter_pass: false,
+                is_complex: false,
             },
             VCFRow {
                 // Edge case of using `RO` and `AO` for coverage
@@ -1306,6 +1328,7 @@ mod tests {
                     ("GT_CONF".to_string(), vec!["3.77".to_string()]),
                 ]),
                 is_filter_pass: false,
+                is_complex: false,
             },
             VCFRow {
                 // Odd edge case which is a valid VCF row where it's a het GT but single COV value
@@ -1320,6 +1343,7 @@ mod tests {
                     ("GT_CONF".to_string(), vec!["613".to_string()]),
                 ]),
                 is_filter_pass: false,
+                is_complex: false,
             },
             VCFRow {
                 // Null call by virtue of failing specific filter
@@ -1334,6 +1358,7 @@ mod tests {
                     ("GT_CONF".to_string(), vec!["613".to_string()]),
                 ]),
                 is_filter_pass: false,
+                is_complex: false,
             },
         ];
         for (idx, record) in expected_records.iter().enumerate() {
@@ -1506,4 +1531,80 @@ mod tests {
             }
         }
     }
+
+    #[test]
+    fn test_complex_is_detected() {
+        // Check that the is_complex flag gets set if a VCF has a complex row in it
+        // This VCF has 1 standard row, then 2 almost complex rows, then a complex row
+        // Standard SNP at 4687
+        // Ref of length 1000 with 2 alts at 4730
+        // Ref of length 1001 with 1 alt at 5730
+        // Ref of length 1001 with 2 alts at 7030 <-- this is the complex row
+
+        let vcf = VCFFile::new("test/complex.vcf".to_string(), false, 3);
+
+        let expected_records = vec![
+            VCFRow {
+                position: 4687,
+                reference: "t".to_string(),
+                alternative: vec!["c".to_string()],
+                filter: vec!["PASS".to_string()],
+                fields: HashMap::from([
+                    ("GT".to_string(), vec!["1/1".to_string()]),
+                    ("DP".to_string(), vec!["68".to_string()]),
+                    ("COV".to_string(), vec!["0".to_string(), "68".to_string()]),
+                    ("GT_CONF".to_string(), vec!["613.77".to_string()]),
+                ]),
+                is_filter_pass: true,is_complex: false,
+            },
+            VCFRow {
+                position: 4730,
+                reference: "aaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaa".to_string(),
+                alternative: vec!["t".to_string(), "g".to_string()],
+                filter: vec!["PASS".to_string()],
+                fields: HashMap::from([
+                    ("GT".to_string(), vec!["1/1".to_string()]),
+                    ("DP".to_string(), vec!["200".to_string()]),
+                    ("COV".to_string(), vec!["1".to_string(), "99".to_string(), "100".to_string()]),
+                    ("GT_CONF".to_string(), vec!["613.77".to_string()]),
+                ]),
+                is_filter_pass: true,is_complex: false,
+            },
+            VCFRow {
+                position: 5730,
+                reference: "aaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaa".to_string(),
+                alternative: vec!["t".to_string()],
+                filter: vec!["PASS".to_string()],
+                fields: HashMap::from([
+                    ("GT".to_string(), vec!["1/1".to_string()]),
+                    ("DP".to_string(), vec!["200".to_string()]),
+                    ("COV".to_string(), vec!["1".to_string(), "99".to_string()]),
+                    ("GT_CONF".to_string(), vec!["613.77".to_string()]),
+                ]),
+                is_filter_pass: true,is_complex: false,
+            },
+            VCFRow {
+                position: 7030,
+                reference: "aaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaa".to_string(),
+                alternative: vec!["t".to_string(), "g".to_string()],
+                filter: vec!["PASS".to_string()],
+                fields: HashMap::from([
+                    ("GT".to_string(), vec!["2/2".to_string()]),
+                    ("DP".to_string(), vec!["200".to_string()]),
+                    ("COV".to_string(), vec!["1".to_string(), "99".to_string(), "100".to_string()]),
+                    ("GT_CONF".to_string(), vec!["613.77".to_string()]),
+                ]),
+                is_filter_pass: true,is_complex: true,
+            },
+        ];
+
+        for (idx, record) in expected_records.iter().enumerate() {
+            assert_eq!(record.position, vcf.records[idx].position);
+            assert_eq!(record.reference, vcf.records[idx].reference);
+            assert_eq!(record.alternative, vcf.records[idx].alternative);
+            assert_eq!(record.filter, vcf.records[idx].filter);
+            assert_eq!(record.fields, vcf.records[idx].fields);
+            assert_eq!(record.is_filter_pass, vcf.records[idx].is_filter_pass);
+        }
+    }
 }

bio_grumpy-1.0.0/test/complex.vcf

@@ -0,0 +1,14 @@
+##fileformat=VCFv4.2
+##source=minos, version 0.4.1
+##fileDate=2018-04-26
+##FORMAT=<ID=COV,Number=R,Type=Integer,Description="Number of reads on ref and alt alleles">
+##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
+##FORMAT=<ID=DP,Number=1,Type=Integer,Description="total kmer depth from gramtools",Source="minos">
+##FORMAT=<ID=GT_CONF,Number=1,Type=Float,Description="Genotype confidence. Difference in log likelihood of most likely and next most likely genotype">
+##INFO=<ID=KMER,Number=1,Type=Integer,Description="Kmer size at which variant was discovered (kmer-size used by gramtools build)">
+##minos_max_read_length=200
+#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	03.vcf
+NC_004148.2	4687	.	T	C	.	PASS	KMER=15	GT:DP:COV:GT_CONF	1/1:68:0,68:613.77
+NC_004148.2	4730	.	AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA	T,G	.	PASS	KMER=15	GT:DP:COV:GT_CONF	1/1:200:1,99,100:613.77
+NC_004148.2	5730	.	AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA	T	.	PASS	KMER=15	GT:DP:COV:GT_CONF	1/1:200:1,99:613.77
+NC_004148.2	7030	.	AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA	T,G	.	PASS	KMER=15	GT:DP:COV:GT_CONF	2/2:200:1,99,100:613.77