Api roll 7: 2014-12-01

discovery/googleapis_beta/genomics__v1beta2.json

Index: discovery/googleapis_beta/genomics__v1beta2.json
diff --git a/discovery/googleapis_beta/genomics__v1beta2.json b/discovery/googleapis_beta/genomics__v1beta2.json
index 9980cdbc4da26645627deb303a9b18f89fb17654..666af1f22649f8be6a7b35d8b1b36fdad8a318c2 100644
--- a/discovery/googleapis_beta/genomics__v1beta2.json
+++ b/discovery/googleapis_beta/genomics__v1beta2.json
@@ -23,7 +23,7 @@
     "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"
@@ -1171,7 +1171,7 @@
             }
         }
     },
-    "revision": "20141112",
+    "revision": "20141113",
     "rootUrl": "https://www.googleapis.com/",
     "schemas": {
         "AlignReadGroupSetsRequest": {
@@ -2012,7 +2012,7 @@
             "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": {
@@ -2024,7 +2024,7 @@
                     "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": {