sequenceserver 1.1.0.beta12 → 2.0.0.beta1

data/spec/sample_reports/no_hits_sample/job.yaml

@@ -1,10 +0,0 @@
---- !ruby/object:SequenceServer::BLAST::Job
-id: no_hits_sample
-method: blastn
-advanced_params: {}
-exitstatus: 0
-
-databases:
-- !ruby/struct:SequenceServer::Database
-  name: "../database/sample/transcripts/Solenopsis_invicta/Sinvicta2-2-3.cdna.subset.fasta"
-  type: nucleotide

data/spec/sample_reports/no_hits_sample/stdout

@@ -1,130 +0,0 @@
-Blast4-archive ::= {
-  request {
-    ident "2.2.30+",
-    body queue-search {
-      program "blastn",
-      service "plain",
-      queries bioseq-set {
-        seq-set {
-          seq {
-            id {
-              local str "Query_1"
-            },
-            descr {
-              user {
-                type str "CFastaReader",
-                data {
-                  {
-                    label str "DefLine",
-                    data str ">"
-                  }
-                }
-              }
-            },
-            inst {
-              repr raw,
-              mol na,
-              length 32,
-              seq-data ncbi2na '39C9155555555555'H
-            }
-          }
-        }
-      },
-      subject database "../database/sample/transcripts/Solenopsis_invicta/Si
-nvicta2-2-3.cdna.subset.fasta",
-      algorithm-options {
-        {
-          name "EvalueThreshold",
-          value cutoff e-value { 1, 10, 1 }
-        },
-        {
-          name "MaskAtHash",
-          value boolean TRUE
-        },
-        {
-          name "DustFilteringLevel",
-          value integer 20
-        },
-        {
-          name "DustFilteringWindow",
-          value integer 64
-        },
-        {
-          name "DustFilteringLinker",
-          value integer 1
-        },
-        {
-          name "UngappedMode",
-          value boolean FALSE
-        },
-        {
-          name "HitlistSize",
-          value integer 500
-        },
-        {
-          name "EffectiveSearchSpace",
-          value big-integer 4482944
-        }
-      },
-      program-options {
-        {
-          name "LCaseMask",
-          value query-mask {
-            locations {
-              packed-int {
-                {
-                  from 9,
-                  to 31,
-                  id local str "Query_1"
-                },
-                {
-                  from 9,
-                  to 31,
-                  id local str "Query_1"
-                }
-              }
-            },
-            frame plus1
-          }
-        }
-      }
-    }
-  },
-  results {
-    alignments {
-    },
-    masks {
-      {
-        locations {
-          packed-int {
-            {
-              from 9,
-              to 31,
-              id local str "Query_1"
-            }
-          }
-        },
-        frame plus1
-      }
-    },
-    ka-blocks {
-      {
-        lambda { 633731443099174, 10, -15 },
-        k { 408145662544724, 10, -15 },
-        h { 91243839227971, 10, -14 },
-        gapped FALSE
-      },
-      {
-        lambda { 625, 10, -3 },
-        k { 41, 10, -2 },
-        h { 78, 10, -2 },
-        gapped TRUE
-      }
-    },
-    search-stats {
-      "Effective search space: 4482944",
-      "Effective search space used: 4482944",
-      "Length adjustment: 16"
-    }
-  }
-}

data/spec/sample_reports/tblastn_sample/job.yaml

@@ -1,10 +0,0 @@
---- !ruby/object:SequenceServer::BLAST::Job
-id: tblastn_sample
-method: tblastn
-advanced_params: {}
-exitstatus: 0
-
-databases:
-- !ruby/struct:SequenceServer::Database
-  name: "../database/sample/transcripts/Solenopsis_invicta/Sinvicta2-2-3.cdna.subset.fasta"
-  type: nucleotide

data/spec/sample_reports/tblastn_sample/stdout

@@ -1,1107 +0,0 @@
-Blast4-archive ::= {
-  request {
-    ident "2.2.30+",
-    body queue-search {
-      program "tblastn",
-      service "plain",
-      queries bioseq-set {
-        seq-set {
-          seq {
-            id {
-              local str "Query_1"
-            },
-            descr {
-              user {
-                type str "CFastaReader",
-                data {
-                  {
-                    label str "DefLine",
-                    data str ">SI2.2.0_06267
- locus=Si_gnF.scaffold02592[1282609..1284114].pep_2 quality=100.00"
-                  }
-                }
-              },
-              title "SI2.2.0_06267
- locus=Si_gnF.scaffold02592[1282609..1284114].pep_2 quality=100.00"
-            },
-            inst {
-              repr raw,
-              mol aa,
-              length 199,
-              seq-data ncbieaa "MNTLWLSLWDYPGKLPLNFMVFDTKDDLQAAYWRDPYSIPLAVIFE
-DPQPISQRLIYEIRTNPSYTLPPPPTKLYSAPISCRKNKTGHWMDDILSIKTGESCPVNNYLHSGFLALQMITDITKI
-KLENSDVTIPDIKLIMFPKEPYTADWMLAFRVVIPLYMVLALSQFITYLLILIVGEKENKIKEGMKMMGLNDSVF"
-            }
-          },
-          seq {
-            id {
-              local str "Query_2"
-            },
-            descr {
-              user {
-                type str "CFastaReader",
-                data {
-                  {
-                    label str "DefLine",
-                    data str ">SI2.2.0_13722
- locus=Si_gnF.scaffold06207[1925625..1928536].pep_1 quality=100.00"
-                  }
-                }
-              },
-              title "SI2.2.0_13722
- locus=Si_gnF.scaffold06207[1925625..1928536].pep_1 quality=100.00"
-            },
-            inst {
-              repr raw,
-              mol aa,
-              length 186,
-              seq-data ncbieaa "MSANRLNVLVTLMLAVALLVTESGNAQVDGYLQFNPKRSAVSSPQK
-YCGKKLSNALQIICDGVYNSMFKKSGQDFPPQNKRHIAHRINGNEEESFTTLKSNFLNWCVEVYHRHYRFVFVSEMEM
-ADYPLAYDISPYLPPFLSRARARGMLDGRFAGRRYRRESRGIHEECCINGCTINELTSYCGP"
-            }
-          }
-        }
-      },
-      subject database "../database/sample/transcripts/Solenopsis_invicta/Si
-nvicta2-2-3.cdna.subset.fasta",
-      algorithm-options {
-        {
-          name "EvalueThreshold",
-          value cutoff e-value { 1, 10, 1 }
-        },
-        {
-          name "DbGeneticCode",
-          value integer 1
-        },
-        {
-          name "UngappedMode",
-          value boolean FALSE
-        },
-        {
-          name "LongestIntronLength",
-          value integer 0
-        },
-        {
-          name "MaskAtHash",
-          value boolean FALSE
-        },
-        {
-          name "SegFilteringWindow",
-          value integer 12
-        },
-        {
-          name "SegFilteringLocut",
-          value real { 22, 10, -1 }
-        },
-        {
-          name "SegFilteringHicut",
-          value real { 25, 10, -1 }
-        },
-        {
-          name "WordThreshold",
-          value integer 13
-        },
-        {
-          name "WindowSize",
-          value integer 40
-        },
-        {
-          name "HitlistSize",
-          value integer 500
-        },
-        {
-          name "CompositionBasedStats",
-          value integer 2
-        },
-        {
-          name "SmithWatermanMode",
-          value boolean FALSE
-        },
-        {
-          name "EffectiveSearchSpace",
-          value big-integer 9254832
-        }
-      }
-    }
-  },
-  results {
-    alignments {
-      {
-        type partial,
-        dim 2,
-        score {
-          {
-            id str "score",
-            value int 1046
-          },
-          {
-            id str "e_value",
-            value real { 991472001167032, 10, -162 }
-          },
-          {
-            id str "bit_score",
-            value real { 407526988689595, 10, -12 }
-          },
-          {
-            id str "num_ident",
-            value int 199
-          },
-          {
-            id str "comp_adjustment_method",
-            value int 2
-          },
-          {
-            id str "num_positives",
-            value int 199
-          },
-          {
-            id str "hsp_percent_coverage",
-            value real { 1, 10, 2 }
-          }
-        },
-        segs std {
-          {
-            dim 2,
-            ids {
-              local str "Query_1",
-              local str "SI2.2.0_06267"
-            },
-            loc {
-              int {
-                from 0,
-                to 198,
-                strand unknown,
-                id local str "Query_1"
-              },
-              int {
-                from 0,
-                to 596,
-                strand plus,
-                id local str "SI2.2.0_06267"
-              }
-            }
-          }
-        }
-      },
-      {
-        type partial,
-        dim 2,
-        score {
-          {
-            id str "score",
-            value int 46
-          },
-          {
-            id str "e_value",
-            value real { 158151944731805, 10, -14 }
-          },
-          {
-            id str "bit_score",
-            value real { 223274127722423, 10, -13 }
-          },
-          {
-            id str "num_ident",
-            value int 9
-          },
-          {
-            id str "comp_adjustment_method",
-            value int 2
-          },
-          {
-            id str "num_positives",
-            value int 15
-          },
-          {
-            id str "hsp_percent_coverage",
-            value real { 135653266331658, 10, -13 }
-          }
-        },
-        segs std {
-          {
-            dim 2,
-            ids {
-              local str "Query_1",
-              local str "SI2.2.0_06904"
-            },
-            loc {
-              int {
-                from 31,
-                to 56,
-                strand unknown,
-                id local str "Query_1"
-              },
-              int {
-                from 117,
-                to 194,
-                strand plus,
-                id local str "SI2.2.0_06904"
-              }
-            }
-          }
-        }
-      },
-      {
-        type partial,
-        dim 2,
-        score {
-          {
-            id str "score",
-            value int 44
-          },
-          {
-            id str "e_value",
-            value real { 264755365382425, 10, -14 }
-          },
-          {
-            id str "bit_score",
-            value real { 215570136204075, 10, -13 }
-          },
-          {
-            id str "num_ident",
-            value int 8
-          },
-          {
-            id str "comp_adjustment_method",
-            value int 2
-          },
-          {
-            id str "num_positives",
-            value int 13
-          },
-          {
-            id str "hsp_percent_coverage",
-            value real { 803768844221105, 10, -14 }
-          }
-        },
-        segs std {
-          {
-            dim 2,
-            ids {
-              local str "Query_1",
-              local str "SI2.2.0_03432"
-            },
-            loc {
-              int {
-                from 50,
-                to 64,
-                strand unknown,
-                id local str "Query_1"
-              },
-              int {
-                from 37,
-                to 81,
-                strand plus,
-                id local str "SI2.2.0_03432"
-              }
-            }
-          }
-        }
-      },
-      {
-        type partial,
-        dim 2,
-        score {
-          {
-            id str "score",
-            value int 42
-          },
-          {
-            id str "e_value",
-            value real { 738402284079177, 10, -14 }
-          },
-          {
-            id str "bit_score",
-            value real { 207866144685728, 10, -13 }
-          },
-          {
-            id str "num_ident",
-            value int 8
-          },
-          {
-            id str "comp_adjustment_method",
-            value int 2
-          },
-          {
-            id str "num_positives",
-            value int 11
-          },
-          {
-            id str "hsp_percent_coverage",
-            value real { 100477386934673, 10, -13 }
-          }
-        },
-        segs std {
-          {
-            dim 2,
-            ids {
-              local str "Query_1",
-              local str "SI2.2.0_05280"
-            },
-            loc {
-              int {
-                from 69,
-                to 87,
-                strand unknown,
-                id local str "Query_1"
-              },
-              int {
-                from 52,
-                to 108,
-                strand minus,
-                id local str "SI2.2.0_05280"
-              }
-            }
-          }
-        }
-      },
-      {
-        type partial,
-        dim 2,
-        score {
-          {
-            id str "score",
-            value int 917
-          },
-          {
-            id str "e_value",
-            value real { 163109526812422, 10, -142 }
-          },
-          {
-            id str "bit_score",
-            value real { 357836243396257, 10, -12 }
-          },
-          {
-            id str "num_ident",
-            value int 170
-          },
-          {
-            id str "comp_adjustment_method",
-            value int 2
-          },
-          {
-            id str "num_positives",
-            value int 170
-          },
-          {
-            id str "hsp_percent_coverage",
-            value real { 1, 10, 2 }
-          }
-        },
-        segs std {
-          {
-            dim 2,
-            ids {
-              local str "Query_2",
-              local str "SI2.2.0_13722"
-            },
-            loc {
-              int {
-                from 0,
-                to 185,
-                strand unknown,
-                id local str "Query_2"
-              },
-              int {
-                from 0,
-                to 557,
-                strand plus,
-                id local str "SI2.2.0_13722"
-              }
-            }
-          }
-        }
-      },
-      {
-        type partial,
-        dim 2,
-        score {
-          {
-            id str "score",
-            value int 70
-          },
-          {
-            id str "e_value",
-            value real { 973505195823272, 10, -18 }
-          },
-          {
-            id str "bit_score",
-            value real { 315722025942587, 10, -13 }
-          },
-          {
-            id str "num_ident",
-            value int 20
-          },
-          {
-            id str "comp_adjustment_method",
-            value int 2
-          },
-          {
-            id str "num_positives",
-            value int 27
-          },
-          {
-            id str "hsp_percent_coverage",
-            value real { 241559139784946, 10, -13 }
-          }
-        },
-        segs std {
-          {
-            dim 2,
-            ids {
-              local str "Query_2",
-              local str "SI2.2.0_13149"
-            },
-            loc {
-              int {
-                from 32,
-                to 42,
-                strand unknown,
-                id local str "Query_2"
-              },
-              int {
-                from 87,
-                to 119,
-                strand plus,
-                id local str "SI2.2.0_13149"
-              }
-            }
-          },
-          {
-            dim 2,
-            ids {
-              local str "Query_2",
-              local str "SI2.2.0_13149"
-            },
-            loc {
-              int {
-                from 43,
-                to 43,
-                strand unknown,
-                id local str "Query_2"
-              },
-              empty local str "SI2.2.0_13149"
-            }
-          },
-          {
-            dim 2,
-            ids {
-              local str "Query_2",
-              local str "SI2.2.0_13149"
-            },
-            loc {
-              int {
-                from 44,
-                to 59,
-                strand unknown,
-                id local str "Query_2"
-              },
-              int {
-                from 120,
-                to 167,
-                strand plus,
-                id local str "SI2.2.0_13149"
-              }
-            }
-          },
-          {
-            dim 2,
-            ids {
-              local str "Query_2",
-              local str "SI2.2.0_13149"
-            },
-            loc {
-              empty local str "Query_2",
-              int {
-                from 168,
-                to 170,
-                strand plus,
-                id local str "SI2.2.0_13149"
-              }
-            }
-          },
-          {
-            dim 2,
-            ids {
-              local str "Query_2",
-              local str "SI2.2.0_13149"
-            },
-            loc {
-              int {
-                from 60,
-                to 75,
-                strand unknown,
-                id local str "Query_2"
-              },
-              int {
-                from 171,
-                to 218,
-                strand plus,
-                id local str "SI2.2.0_13149"
-              }
-            }
-          }
-        }
-      },
-      {
-        type partial,
-        dim 2,
-        score {
-          {
-            id str "score",
-            value int 64
-          },
-          {
-            id str "e_value",
-            value real { 591430689703162, 10, -17 }
-          },
-          {
-            id str "bit_score",
-            value real { 292610051387546, 10, -13 }
-          },
-          {
-            id str "num_ident",
-            value int 10
-          },
-          {
-            id str "comp_adjustment_method",
-            value int 2
-          },
-          {
-            id str "num_positives",
-            value int 15
-          },
-          {
-            id str "hsp_percent_coverage",
-            value real { 123279569892473, 10, -13 }
-          }
-        },
-        segs std {
-          {
-            dim 2,
-            ids {
-              local str "Query_2",
-              local str "SI2.2.0_13149"
-            },
-            loc {
-              int {
-                from 164,
-                to 185,
-                strand unknown,
-                id local str "Query_2"
-              },
-              int {
-                from 237,
-                to 302,
-                strand plus,
-                id local str "SI2.2.0_13149"
-              }
-            }
-          }
-        }
-      },
-      {
-        type partial,
-        dim 2,
-        score {
-          {
-            id str "score",
-            value int 48
-          },
-          {
-            id str "e_value",
-            value real { 489490109366324, 10, -15 }
-          },
-          {
-            id str "bit_score",
-            value real { 23097811924077, 10, -12 }
-          },
-          {
-            id str "num_ident",
-            value int 13
-          },
-          {
-            id str "comp_adjustment_method",
-            value int 2
-          },
-          {
-            id str "num_positives",
-            value int 17
-          },
-          {
-            id str "hsp_percent_coverage",
-            value real { 160913978494624, 10, -13 }
-          }
-        },
-        segs std {
-          {
-            dim 2,
-            ids {
-              local str "Query_2",
-              local str "SI2.2.0_09379"
-            },
-            loc {
-              int {
-                from 58,
-                to 72,
-                strand unknown,
-                id local str "Query_2"
-              },
-              int {
-                from 103,
-                to 147,
-                strand minus,
-                id local str "SI2.2.0_09379"
-              }
-            }
-          },
-          {
-            dim 2,
-            ids {
-              local str "Query_2",
-              local str "SI2.2.0_09379"
-            },
-            loc {
-              int {
-                from 73,
-                to 73,
-                strand unknown,
-                id local str "Query_2"
-              },
-              empty local str "SI2.2.0_09379"
-            }
-          },
-          {
-            dim 2,
-            ids {
-              local str "Query_2",
-              local str "SI2.2.0_09379"
-            },
-            loc {
-              int {
-                from 74,
-                to 86,
-                strand unknown,
-                id local str "Query_2"
-              },
-              int {
-                from 64,
-                to 102,
-                strand minus,
-                id local str "SI2.2.0_09379"
-              }
-            }
-          }
-        }
-      },
-      {
-        type partial,
-        dim 2,
-        score {
-          {
-            id str "score",
-            value int 45
-          },
-          {
-            id str "e_value",
-            value real { 724328385986037, 10, -15 }
-          },
-          {
-            id str "bit_score",
-            value real { 219422131963249, 10, -13 }
-          },
-          {
-            id str "num_ident",
-            value int 7
-          },
-          {
-            id str "comp_adjustment_method",
-            value int 1
-          },
-          {
-            id str "num_positives",
-            value int 14
-          },
-          {
-            id str "hsp_percent_coverage",
-            value real { 117903225806452, 10, -13 }
-          }
-        },
-        segs std {
-          {
-            dim 2,
-            ids {
-              local str "Query_2",
-              local str "SI2.2.0_02019"
-            },
-            loc {
-              int {
-                from 119,
-                to 139,
-                strand unknown,
-                id local str "Query_2"
-              },
-              int {
-                from 46,
-                to 108,
-                strand minus,
-                id local str "SI2.2.0_02019"
-              }
-            }
-          }
-        }
-      },
-      {
-        type partial,
-        dim 2,
-        score {
-          {
-            id str "score",
-            value int 48
-          },
-          {
-            id str "e_value",
-            value real { 137339689136456, 10, -14 }
-          },
-          {
-            id str "bit_score",
-            value real { 23097811924077, 10, -12 }
-          },
-          {
-            id str "num_ident",
-            value int 14
-          },
-          {
-            id str "comp_adjustment_method",
-            value int 2
-          },
-          {
-            id str "num_positives",
-            value int 25
-          },
-          {
-            id str "hsp_percent_coverage",
-            value real { 252311827956989, 10, -13 }
-          }
-        },
-        segs std {
-          {
-            dim 2,
-            ids {
-              local str "Query_2",
-              local str "SI2.2.0_03352"
-            },
-            loc {
-              int {
-                from 41,
-                to 52,
-                strand unknown,
-                id local str "Query_2"
-              },
-              int {
-                from 495,
-                to 530,
-                strand plus,
-                id local str "SI2.2.0_03352"
-              }
-            }
-          },
-          {
-            dim 2,
-            ids {
-              local str "Query_2",
-              local str "SI2.2.0_03352"
-            },
-            loc {
-              empty local str "Query_2",
-              int {
-                from 531,
-                to 551,
-                strand plus,
-                id local str "SI2.2.0_03352"
-              }
-            }
-          },
-          {
-            dim 2,
-            ids {
-              local str "Query_2",
-              local str "SI2.2.0_03352"
-            },
-            loc {
-              int {
-                from 53,
-                to 86,
-                strand unknown,
-                id local str "Query_2"
-              },
-              int {
-                from 552,
-                to 653,
-                strand plus,
-                id local str "SI2.2.0_03352"
-              }
-            }
-          }
-        }
-      },
-      {
-        type partial,
-        dim 2,
-        score {
-          {
-            id str "score",
-            value int 44
-          },
-          {
-            id str "e_value",
-            value real { 3025295033467, 10, -12 }
-          },
-          {
-            id str "bit_score",
-            value real { 215570136204075, 10, -13 }
-          },
-          {
-            id str "num_ident",
-            value int 22
-          },
-          {
-            id str "comp_adjustment_method",
-            value int 2
-          },
-          {
-            id str "num_positives",
-            value int 32
-          },
-          {
-            id str "hsp_percent_coverage",
-            value real { 354462365591398, 10, -13 }
-          }
-        },
-        segs std {
-          {
-            dim 2,
-            ids {
-              local str "Query_2",
-              local str "SI2.2.0_05451"
-            },
-            loc {
-              int {
-                from 97,
-                to 115,
-                strand unknown,
-                id local str "Query_2"
-              },
-              int {
-                from 26,
-                to 82,
-                strand plus,
-                id local str "SI2.2.0_05451"
-              }
-            }
-          },
-          {
-            dim 2,
-            ids {
-              local str "Query_2",
-              local str "SI2.2.0_05451"
-            },
-            loc {
-              empty local str "Query_2",
-              int {
-                from 83,
-                to 130,
-                strand plus,
-                id local str "SI2.2.0_05451"
-              }
-            }
-          },
-          {
-            dim 2,
-            ids {
-              local str "Query_2",
-              local str "SI2.2.0_05451"
-            },
-            loc {
-              int {
-                from 116,
-                to 125,
-                strand unknown,
-                id local str "Query_2"
-              },
-              int {
-                from 131,
-                to 160,
-                strand plus,
-                id local str "SI2.2.0_05451"
-              }
-            }
-          },
-          {
-            dim 2,
-            ids {
-              local str "Query_2",
-              local str "SI2.2.0_05451"
-            },
-            loc {
-              int {
-                from 126,
-                to 138,
-                strand unknown,
-                id local str "Query_2"
-              },
-              empty local str "SI2.2.0_05451"
-            }
-          },
-          {
-            dim 2,
-            ids {
-              local str "Query_2",
-              local str "SI2.2.0_05451"
-            },
-            loc {
-              int {
-                from 139,
-                to 148,
-                strand unknown,
-                id local str "Query_2"
-              },
-              int {
-                from 161,
-                to 190,
-                strand plus,
-                id local str "SI2.2.0_05451"
-              }
-            }
-          },
-          {
-            dim 2,
-            ids {
-              local str "Query_2",
-              local str "SI2.2.0_05451"
-            },
-            loc {
-              int {
-                from 149,
-                to 154,
-                strand unknown,
-                id local str "Query_2"
-              },
-              empty local str "SI2.2.0_05451"
-            }
-          },
-          {
-            dim 2,
-            ids {
-              local str "Query_2",
-              local str "SI2.2.0_05451"
-            },
-            loc {
-              int {
-                from 155,
-                to 161,
-                strand unknown,
-                id local str "Query_2"
-              },
-              int {
-                from 191,
-                to 211,
-                strand plus,
-                id local str "SI2.2.0_05451"
-              }
-            }
-          }
-        }
-      },
-      {
-        type partial,
-        dim 2,
-        score {
-          {
-            id str "score",
-            value int 41
-          },
-          {
-            id str "e_value",
-            value real { 665464998703274, 10, -14 }
-          },
-          {
-            id str "bit_score",
-            value real { 204014148926555, 10, -13 }
-          },
-          {
-            id str "num_ident",
-            value int 8
-          },
-          {
-            id str "comp_adjustment_method",
-            value int 2
-          },
-          {
-            id str "num_positives",
-            value int 14
-          },
-          {
-            id str "hsp_percent_coverage",
-            value real { 101774193548387, 10, -13 }
-          }
-        },
-        segs std {
-          {
-            dim 2,
-            ids {
-              local str "Query_2",
-              local str "SI2.2.0_05852"
-            },
-            loc {
-              int {
-                from 141,
-                to 158,
-                strand unknown,
-                id local str "Query_2"
-              },
-              int {
-                from 192,
-                to 245,
-                strand minus,
-                id local str "SI2.2.0_05852"
-              }
-            }
-          }
-        }
-      }
-    },
-    masks {
-      {
-        locations {
-          packed-int {
-            {
-              from 5,
-              to 20,
-              id local str "Query_2"
-            }
-          }
-        },
-        frame notset
-      }
-    },
-    ka-blocks {
-      {
-        lambda { 322429245874507, 10, -15 },
-        k { 139801292049695, 10, -15 },
-        h { 436862255107731, 10, -15 },
-        gapped FALSE
-      },
-      {
-        lambda { 267, 10, -3 },
-        k { 41, 10, -3 },
-        h { 14, 10, -2 },
-        gapped TRUE
-      }
-    },
-    search-stats {
-      "Effective search space: 9254832",
-      "Effective search space used: 9254832",
-      "Length adjustment: 61"
-    }
-  }
-}