Update docs for 1.4.1 release
diff --git a/docs/dyn/genomics_v1beta2.reads.html b/docs/dyn/genomics_v1beta2.reads.html
index 8b2b960..777cbeb 100644
--- a/docs/dyn/genomics_v1beta2.reads.html
+++ b/docs/dyn/genomics_v1beta2.reads.html
@@ -117,7 +117,7 @@
# out = "" 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
# Converting 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).
# cigarMap = { "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
- "info": { # A map of additional read alignment information.
+ "info": { # A string which maps to an array of values.
"a_key": [ # A string which maps to an array of values.
"A String",
],
@@ -131,7 +131,7 @@
"fragmentName": "A String", # The fragment name. Equivalent to QNAME (query template name) in SAM.
"readNumber": 42, # The read number in sequencing. 0-based and less than numberReads. This field replaces SAM flag 0x40 and 0x80.
"properPlacement": True or False, # The orientation and the distance between reads from the fragment are consistent with the sequencing protocol (SAM flag 0x2)
- "nextMatePosition": { # An abstraction for referring to a genomic position, in relation to some already known reference. For now, represents a genomic position as a reference name, a base number on that reference (0-based), and a determination of forward or reverse strand. # The mapping of the primary alignment of the (readNumber+1)%numberReads read in the fragment. It replaces mate position and mate strand in SAM.
+ "nextMatePosition": { # An abstraction for referring to a genomic position, in relation to some already known reference. For now, represents a genomic position as a reference name, a base number on that reference (0-based), and a determination of forward or reverse strand. # The position of the primary alignment of the (readNumber+1)%numberReads read in the fragment. It replaces mate position and mate strand in SAM. This field will be unset if that read is unmapped or if the fragment only has a single read.
"position": "A String", # The 0-based offset from the start of the forward strand for that reference.
"reverseStrand": True or False, # Whether this position is on the reverse strand, as opposed to the forward strand.
"referenceName": "A String", # The name of the reference in whatever reference set is being used.
@@ -142,7 +142,7 @@
"secondaryAlignment": True or False, # Whether this alignment is secondary. Equivalent to SAM flag 0x100. A secondary alignment represents an alternative to the primary alignment for this read. Aligners may return secondary alignments if a read can map ambiguously to multiple coordinates in the genome. By convention, each read has one and only one alignment where both secondaryAlignment and supplementaryAlignment are false.
"alignedSequence": "A String", # 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.
"id": "A String", # The unique ID for this read. This is a generated unique ID, not to be confused with fragmentName.
- "alignment": { # A linear alignment can be represented by one CIGAR string. Describes the mapped position and local alignment of the read to the reference. # The linear alignment for this alignment record. This field will be null if the read is unmapped.
+ "alignment": { # A linear alignment can be represented by one CIGAR string. Describes the mapped position and local alignment of the read to the reference. # The linear alignment for this alignment record. This field will be unset if the read is unmapped.
"position": { # An abstraction for referring to a genomic position, in relation to some already known reference. For now, represents a genomic position as a reference name, a base number on that reference (0-based), and a determination of forward or reverse strand. # The position of this alignment.
"position": "A String", # The 0-based offset from the start of the forward strand for that reference.
"reverseStrand": True or False, # Whether this position is on the reverse strand, as opposed to the forward strand.