Api roll 7: 2014-12-01

discovery/googleapis_beta/genomics__v1beta2.json

 {
     "auth": {
         "oauth2": {
             "scopes": {
                 "https://www.googleapis.com/auth/bigquery": {
                     "description": "View and manage your data in Google BigQuery"
                 },
                 "https://www.googleapis.com/auth/devstorage.read_write": {
                     "description": "Manage your data in Google Cloud Storage"
                 },
                 "https://www.googleapis.com/auth/genomics": {
                     "description": "View and manage Genomics data"
                 },
                 "https://www.googleapis.com/auth/genomics.readonly": {
                     "description": "View Genomics data"
                 }
             }
         }
     },
     "basePath": "/genomics/v1beta2/",
     "baseUrl": "https://www.googleapis.com/genomics/v1beta2/",
     "batchPath": "batch",
     "description": "Provides access to Genomics data.",
     "discoveryVersion": "v1",
     "documentationLink": "https://developers.google.com/genomics/v1beta2/reference",
-    "etag": "\"l66ggWbucbkBw9Lpos72oziyefE/6ckREvRjfWsdC7sKQKylGfPy3tY\"",
+    "etag": "\"ye6orv2F-1npMW3u9suM3a7C5Bo/B0U3dL3DEjo6LTLutBKsRG1fa1o\"",
     "icons": {
         "x16": "http://www.google.com/images/icons/product/search-16.gif",
         "x32": "http://www.google.com/images/icons/product/search-32.gif"
     },
     "id": "genomics:v1beta2",
     "kind": "discovery#restDescription",
     "name": "genomics",
     "ownerDomain": "google.com",
     "ownerName": "Google",
     "parameters": {
@@ skipping 1127 matching lines @@
                     "response": {
                         "$ref": "VariantSet"
                     },
                     "scopes": [
                         "https://www.googleapis.com/auth/genomics"
                     ]
                 }
             }
         }
     },
-    "revision": "20141112",
+    "revision": "20141113",
     "rootUrl": "https://www.googleapis.com/",
     "schemas": {
         "AlignReadGroupSetsRequest": {
             "description": "The read group set align request.",
             "id": "AlignReadGroupSetsRequest",
             "properties": {
                 "bamSourceUris": {
                     "description": "The BAM source files for alignment. Exactly one of readGroupSetIds, bamSourceUris, interleavedFastqSource or pairedFastqSource must be provided. The caller must have READ permissions for these files.",
                     "items": {
                         "type": "string"
@@ skipping 820 matching lines @@
                 },
                 "start": {
                     "description": "The start position of the range on the reference, 0-based inclusive. If specified, referenceName must also be specified.",
                     "format": "int64",
                     "type": "string"
                 }
             },
             "type": "object"
         },
         "Read": {
-            "description": "A read alignment describes a linear alignment of a string of DNA to a reference sequence, in addition to metadata about the fragment (the molecule of DNA sequenced) and the read (the bases which were read by the sequencer). A read is equivalent to a line in a SAM file. A read belongs to exactly one read group and exactly one read group set.",
+            "description": "A read alignment describes a linear alignment of a string of DNA to a reference sequence, in addition to metadata about the fragment (the molecule of DNA sequenced) and the read (the bases which were read by the sequencer). A read is equivalent to a line in a SAM file. A read belongs to exactly one read group and exactly one read group set. Generating a reference-aligned sequence string When interacting with mapped reads, it's often useful to produce a string representing the local alignment of the read to reference. The following pseudocode demonstrates one way of doing this:\nout = \"\" offset = 0 for c in read.alignment.cigar { switch c.operation { case \"ALIGNMENT_MATCH\", \"SEQUENCE_MATCH\", \"SEQUENCE_MISMATCH\": out += read.alignedSequence[offset:offset+c.operationLength] offset += c.operationLength break case \"CLIP_SOFT\", \"INSERT\": offset += c.operationLength break case \"PAD\": out += repeat(\"*\", c.operationLength) break case \"DELETE\": out += repeat(\"-\", c.operationLength) break case \"SKIP\": out += repeat(\" \", c.operationLength) break case \"CLIP_HARD\": break } } return out\nConverting to SAM's CIGAR string The following pseudocode generates a SAM CIGAR string from the cigar field. Note that this is a lossy conversion (cigar.referenceSequence is lost).\ncigarMap = { \"ALIGNMENT_MATCH\": \"M\", \"INSERT\": \"I\", \"DELETE\": \"D\", \"SKIP\": \"N\", \"CLIP_SOFT\": \"S\", \"CLIP_HARD\": \"H\", \"PAD\": \"P\", \"SEQUENCE_MATCH\": \"=\", \"SEQUENCE_MISMATCH\": \"X\", } cigarStr = \"\" for c in read.alignment.cigar { cigarStr += c.operationLength + cigarMap[c.operation] } return cigarStr",
             "id": "Read",
             "properties": {
                 "alignedQuality": {
                     "description": "The quality of the read sequence contained in this alignment record. alignedSequence and alignedQuality may be shorter than the full read sequence and quality. This will occur if the alignment is part of a chimeric alignment, or if the read was trimmed. When this occurs, the CIGAR for this read will begin/end with a hard clip operator that will indicate the length of the excised sequence.",
                     "items": {
                         "format": "int32",
                         "type": "integer"
                     },
                     "type": "array"
                 },
                 "alignedSequence": {
-                    "description": "The bases of the read sequence contained in this alignment record. alignedSequence and alignedQuality may be shorter than the full read sequence and quality. This will occur if the alignment is part of a chimeric alignment, or if the read was trimmed. When this occurs, the CIGAR for this read will begin/end with a hard clip operator that will indicate the length of the excised sequence.",
+                    "description": "The bases of the read sequence contained in this alignment record, without CIGAR operations applied. alignedSequence and alignedQuality may be shorter than the full read sequence and quality. This will occur if the alignment is part of a chimeric alignment, or if the read was trimmed. When this occurs, the CIGAR for this read will begin/end with a hard clip operator that will indicate the length of the excised sequence.",
                     "type": "string"
                 },
                 "alignment": {
                     "$ref": "LinearAlignment",
                     "description": "The linear alignment for this alignment record. This field will be null if the read is unmapped."
                 },
                 "duplicateFragment": {
                     "description": "The fragment is a PCR or optical duplicate (SAM flag 0x400)",
                     "type": "boolean"
                 },
@@ skipping 848 matching lines @@
                     "type": "array"
                 }
             },
             "type": "object"
         }
     },
     "servicePath": "genomics/v1beta2/",
     "title": "Genomics API",
     "version": "v1beta2"
 }