Api roll 6: 2014-11-17

generated/googleapis_beta/lib/genomics/v1beta2.dart

 library googleapis_beta.genomics.v1beta2;
 
 import "dart:core" as core;
 import "dart:collection" as collection;
 import "dart:async" as async;
 import "dart:convert" as convert;
 
 import "package:crypto/crypto.dart" as crypto;
 import 'package:http/http.dart' as http;
 import '../src/common_internal.dart' as common_internal;
@@ skipping 2357 matching lines @@
    * represented the heterozygous value CA for this variant. If the genotype was
    * instead [0, 1], the represented value would be TA. Ordering of the genotype
    * values is important if the phaseset is present. If a genotype is not called
    * (that is, a . is present in the GT string) -1 is returned.
    */
   core.List<core.int> genotype;
 
   /**
    * The genotype likelihoods for this variant call. Each array entry represents
    * how likely a specific genotype is for this call. The value ordering is
-   * defined by the GL tag in the VCF spec.
+   * defined by the GL tag in the VCF spec. If Phred-scaled genotype likelihood
+   * scores (PL) are available and log10(P) genotype likelihood scores (GL) are
+   * not, PL scores are converted to GL scores. If both are available, PL scores
+   * are stored in info.
    */
   core.List<core.double> genotypeLikelihood;
 
   /** A map of additional variant call information. */
   core.Map<core.String, core.List<core.String>> info;
 
   /**
    * If this field is present, this variant call's genotype ordering implies the
    * phase of the bases and is consistent with any other variant calls in the
    * same reference sequence which have the same phaseset value. When importing
@@ skipping 1602 matching lines @@
    * The mapping of the primary alignment of the (readNumber+1)%numberReads read
    * in the fragment. It replaces mate position and mate strand in SAM.
    */
   Position nextMatePosition;
 
   /** The number of reads in the fragment (extension to SAM flag 0x1). */
   core.int numberReads;
 
   /**
    * The orientation and the distance between reads from the fragment are
-   * consistent with the sequencing protocol (extension to SAM flag 0x2)
+   * consistent with the sequencing protocol (SAM flag 0x2)
    */
   core.bool properPlacement;
 
   /**
    * The ID of the read group this read belongs to. (Every read must belong to
    * exactly one read group.)
    */
   core.String readGroupId;
 
   /**
@@ skipping 1851 matching lines @@
       _json["metadata"] = metadata.map((value) => (value).toJson()).toList();
     }
     if (referenceBounds != null) {
       _json["referenceBounds"] = referenceBounds.map((value) => (value).toJson()).toList();
     }
     return _json;
   }
 }