Add specs and example BAMlet

COPYRIGHT.txt

@@ -208,3 +208,28 @@ zlib 1.2.8
   2. Altered source versions must be plainly marked as such, and must not be
      misrepresented as being the original software.
   3. This notice may not be removed or altered from any source distribution.
+
+******************************************************************
+
+JSON for Modern C++ https://nlohmann.github.io/json/
+
+The class is licensed under the MIT License:
+
+Copyright (C) 2013-2017 Niels Lohmann
+
+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 rights 
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell 
+copies of the Software, and to permit persons to whom the Software is 
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all 
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED “AS IS”, WITHOUT WARRANTY OF ANY KIND, EXPRESS OR 
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS 
+FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR 
+COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN 
+AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION 
+WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.

data/examples/hg19/README.txt

@@ -0,0 +1,16 @@
+
+Expansion Hunter can be run on the example BAMlet using the following command
+after replacing "hg19_ref.fa" with a path to hg19 reference FASTA file and 
+adjusting paths in the remaining command line arguments as approprite.
+
+Note that "read-depth" must be specified when running Expansion Hunter on an
+incomplete BAM file.
+
+ExpansionHunter \
+  --bam bamlets/bamlet.bam \
+  --ref-fasta hg19_ref.fa \
+  --repeat-specs ../../repeat-specs/hg19/ \
+  --vcf output/bamlet.vcf \
+  --json output/bamlet.json \
+  --log output/bamlet.log \
+  --read-depth 30

data/examples/hg19/output/bamlet.json

@@ -0,0 +1,266 @@
+{
+    "AR": {
+        "AnchoredIrrCount": 0,
+        "Genotype": "24/25",
+        "GenotypeCi": "24-24/25-25",
+        "GenotypeSupport": "10-20-0/5-20-0",
+        "IrrCount": 0,
+        "RepeatId": "AR",
+        "RepeatSizes": {
+            "Repeat1": {
+                "NumSupportingReads": 10,
+                "Size": 24,
+                "Source": "SPANNING"
+            },
+            "Repeat2": {
+                "NumSupportingReads": 5,
+                "Size": 25,
+                "Source": "SPANNING"
+            }
+        },
+        "RepeatUnit": "GCA",
+        "TargetRegion": "chrX:66765159-66765227",
+        "UnalignedIrrCount": 0
+    },
+    "ATN1": {
+        "AnchoredIrrCount": 0,
+        "Genotype": "12/14",
+        "GenotypeCi": "12-12/14-14",
+        "GenotypeSupport": "13-9-0/22-9-0",
+        "IrrCount": 0,
+        "RepeatId": "ATN1",
+        "RepeatSizes": {
+            "Repeat1": {
+                "NumSupportingReads": 13,
+                "Size": 12,
+                "Source": "SPANNING"
+            },
+            "Repeat2": {
+                "NumSupportingReads": 22,
+                "Size": 14,
+                "Source": "SPANNING"
+            }
+        },
+        "RepeatUnit": "CAG",
+        "TargetRegion": "chr12:7045880-7045936",
+        "UnalignedIrrCount": 0
+    },
+    "ATXN1": {
+        "AnchoredIrrCount": 0,
+        "Genotype": "30/37",
+        "GenotypeCi": "30-30/37-37",
+        "GenotypeSupport": "10-42-0/4-42-0",
+        "IrrCount": 0,
+        "RepeatId": "ATXN1",
+        "RepeatSizes": {
+            "Repeat1": {
+                "NumSupportingReads": 10,
+                "Size": 30,
+                "Source": "SPANNING"
+            },
+            "Repeat2": {
+                "NumSupportingReads": 4,
+                "Size": 37,
+                "Source": "SPANNING"
+            }
+        },
+        "RepeatUnit": "TGC",
+        "TargetRegion": "chr6:16327865-16327954",
+        "UnalignedIrrCount": 0
+    },
+    "ATXN3": {
+        "AnchoredIrrCount": 0,
+        "Genotype": "24/24",
+        "GenotypeCi": "24-24/24-24",
+        "GenotypeSupport": "10-15-0/10-15-0",
+        "IrrCount": 0,
+        "RepeatId": "ATXN3",
+        "RepeatSizes": {
+            "Repeat1": {
+                "NumSupportingReads": 10,
+                "Size": 24,
+                "Source": "SPANNING"
+            }
+        },
+        "RepeatUnit": "GCT",
+        "TargetRegion": "chr14:92537354-92537386",
+        "UnalignedIrrCount": 0
+    },
+    "BamStats": {
+        "MedianDepth": 30.0,
+        "ReadLength": 150
+    },
+    "C9ORF72": {
+        "AnchoredIrrCount": 0,
+        "Genotype": "2/8",
+        "GenotypeCi": "2-2/8-8",
+        "GenotypeSupport": "9-5-0/6-7-0",
+        "IrrCount": 0,
+        "OffTargetRegionIrrCounts": {
+            "chr11:2905960-2906190": 0,
+            "chr11:44748502-44748739": 0,
+            "chr11:910821-910969": 0,
+            "chr12:128751638-128751649": 0,
+            "chr12:54476278-54476439": 0,
+            "chr13:107569867-107570000": 0,
+            "chr16:49526377-49526380": 0,
+            "chr16:819162-819226": 0,
+            "chr18:74203223-74203243": 0,
+            "chr19:39897404-39897410": 0,
+            "chr19:878803-878954": 0,
+            "chr1:150552238-150552273": 0,
+            "chr20:388475-388656": 0,
+            "chr20:60640211-60640346": 0,
+            "chr22:51066608-51066626": 0,
+            "chr2:240659782-240660010": 0,
+            "chr3:49591993-49592173": 0,
+            "chr3:50161662-50161732": 0,
+            "chr5:10761494-10761495": 0,
+            "chr5:176797951-176798133": 0,
+            "chr6:109804703-109804748": 0,
+            "chr6:33601522-33601525": 0,
+            "chr9:132331488-132331496": 0,
+            "chr9:132428311-132428437": 0,
+            "chrX:153569931-153569996": 0,
+            "chrX:153618748-153618918": 0,
+            "chrX:49644488-49644585": 0,
+            "chrX:53652706-53652891": 0,
+            "chrX:9754276-9754424": 0
+        },
+        "RepeatId": "C9ORF72",
+        "RepeatSizes": {
+            "Repeat1": {
+                "NumSupportingReads": 9,
+                "Size": 2,
+                "Source": "SPANNING"
+            },
+            "Repeat2": {
+                "NumSupportingReads": 6,
+                "Size": 8,
+                "Source": "SPANNING"
+            }
+        },
+        "RepeatUnit": "GGCCCC",
+        "TargetRegion": "chr9:27573527-27573544",
+        "UnalignedIrrCount": 0
+    },
+    "DMPK": {
+        "AnchoredIrrCount": 0,
+        "Genotype": "5/11",
+        "GenotypeCi": "5-5/11-11",
+        "GenotypeSupport": "20-8-0/11-13-0",
+        "IrrCount": 0,
+        "RepeatId": "DMPK",
+        "RepeatSizes": {
+            "Repeat1": {
+                "NumSupportingReads": 20,
+                "Size": 5,
+                "Source": "SPANNING"
+            },
+            "Repeat2": {
+                "NumSupportingReads": 11,
+                "Size": 11,
+                "Source": "SPANNING"
+            }
+        },
+        "RepeatUnit": "CAG",
+        "TargetRegion": "chr19:46273463-46273522",
+        "UnalignedIrrCount": 0
+    },
+    "FMR1": {
+        "AnchoredIrrCount": 0,
+        "Genotype": "23/30",
+        "GenotypeCi": "23-23/30-30",
+        "GenotypeSupport": "5-4-0/5-6-0",
+        "IrrCount": 0,
+        "OffTargetRegionIrrCounts": {
+            "chr10:101295193-101295194": 0,
+            "chr12:125052155-125052156": 0,
+            "chr12:7781291-7781350": 0,
+            "chr16:25703614-25703635": 0,
+            "chr16:28074517-28074518": 0,
+            "chr17:30814025-30814026": 0,
+            "chr17:64298468-64298469": 0,
+            "chr19:2015525-2015526": 0,
+            "chr20:30865501-30865516": 0,
+            "chr2:211036021-211036032": 0,
+            "chr2:225449879-225449880": 0,
+            "chr2:87141541-87141618": 0,
+            "chr2:92230910-92230911": 0,
+            "chr5:443335-443364": 0,
+            "chr7:100271438-100271439": 0,
+            "chr7:104654598-104654599": 0,
+            "chr7:143059854-143059855": 0,
+            "chr7:20824940-20824941": 0,
+            "chr9:100616696-100616697": 0,
+            "chrX:20009037-20009046": 0
+        },
+        "RepeatId": "FMR1",
+        "RepeatSizes": {
+            "Repeat1": {
+                "NumSupportingReads": 1,
+                "Size": 8,
+                "Source": "SPANNING"
+            },
+            "Repeat2": {
+                "NumSupportingReads": 5,
+                "Size": 23,
+                "Source": "SPANNING"
+            },
+            "Repeat3": {
+                "NumSupportingReads": 5,
+                "Size": 30,
+                "Source": "SPANNING"
+            }
+        },
+        "RepeatUnit": "CGG",
+        "TargetRegion": "chrX:146993569-146993628",
+        "UnalignedIrrCount": 0
+    },
+    "FXN": {
+        "AnchoredIrrCount": 0,
+        "Genotype": "9/9",
+        "GenotypeCi": "9-9/9-9",
+        "GenotypeSupport": "10-4-0/10-4-0",
+        "IrrCount": 0,
+        "RepeatId": "FXN",
+        "RepeatSizes": {
+            "Repeat1": {
+                "NumSupportingReads": 10,
+                "Size": 9,
+                "Source": "SPANNING"
+            }
+        },
+        "RepeatUnit": "GAA",
+        "TargetRegion": "chr9:71652203-71652220",
+        "UnalignedIrrCount": 0
+    },
+    "HTT": {
+        "AnchoredIrrCount": 0,
+        "Genotype": "10/20",
+        "GenotypeCi": "10-10/20-20",
+        "GenotypeSupport": "5-14-0/12-18-0",
+        "IrrCount": 0,
+        "RepeatId": "HTT",
+        "RepeatSizes": {
+            "Repeat1": {
+                "NumSupportingReads": 5,
+                "Size": 10,
+                "Source": "SPANNING"
+            },
+            "Repeat2": {
+                "NumSupportingReads": 1,
+                "Size": 17,
+                "Source": "SPANNING"
+            },
+            "Repeat3": {
+                "NumSupportingReads": 12,
+                "Size": 20,
+                "Source": "SPANNING"
+            }
+        },
+        "RepeatUnit": "CAG",
+        "TargetRegion": "chr4:3076604-3076660",
+        "UnalignedIrrCount": 0
+    }
+}