Clean and regen docs (#401)
diff --git a/docs/dyn/genomics_v1.reads.html b/docs/dyn/genomics_v1.reads.html
index e8c2fb7..2fbe447 100644
--- a/docs/dyn/genomics_v1.reads.html
+++ b/docs/dyn/genomics_v1.reads.html
@@ -122,11 +122,11 @@
],
"pageSize": 42, # The maximum number of results to return in a single page. If unspecified,
# defaults to 256. The maximum value is 2048.
+ "start": "A String", # The start position of the range on the reference, 0-based inclusive. If
+ # specified, `referenceName` must also be specified.
"pageToken": "A String", # The continuation token, which is used to page through large result sets.
# To get the next page of results, set this parameter to the value of
# `nextPageToken` from the previous response.
- "start": "A String", # The start position of the range on the reference, 0-based inclusive. If
- # specified, `referenceName` must also be specified.
"referenceName": "A String", # The reference sequence name, for example `chr1`, `1`, or `chrX`. If set to
# `*`, only unmapped reads are returned. If unspecified, all reads (mapped
# and unmapped) are returned.
@@ -243,17 +243,6 @@
],
},
"duplicateFragment": True or False, # The fragment is a PCR or optical duplicate (SAM flag 0x400).
- "nextMatePosition": { # An abstraction for referring to a genomic position, in relation to some # The mapping of the primary alignment of the
- # `(readNumber+1)%numberReads` read in the fragment. It replaces
- # mate position and mate strand in SAM.
- # 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.
- "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.
- },
"readGroupSetId": "A String", # The ID of the read group set this read belongs to. A read belongs to
# exactly one read group set.
"alignedQuality": [ # The quality of the read sequence contained in this alignment record
@@ -268,8 +257,8 @@
"failedVendorQualityChecks": True or False, # Whether this read did not pass filters, such as platform or vendor quality
# controls (SAM flag 0x200).
"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.
+ "id": "A String", # The server-generated read ID, unique across all reads. This is different
+ # from the `fragmentName`.
"properPlacement": True or False, # The orientation and the distance between reads from the fragment are
# consistent with the sequencing protocol (SAM flag 0x2).
"readGroupId": "A String", # The ID of the read group this read belongs to. A read belongs to exactly
@@ -289,6 +278,12 @@
# represent the bases for its respective linear alignment.
"numberReads": 42, # The number of reads in the fragment (extension to SAM flag 0x1).
"fragmentLength": 42, # The observed length of the fragment, equivalent to TLEN in SAM.
+ "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** (equivalent to SEQ in SAM).
# `alignedSequence` and `alignedQuality` may be
@@ -296,8 +291,8 @@
# 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 server-generated read ID, unique across all reads. This is different
- # from the `fragmentName`.
+ "readNumber": 42, # The read number in sequencing. 0-based and less than numberReads. This
+ # field replaces SAM flag 0x40 and 0x80.
"alignment": { # A linear alignment can be represented by one CIGAR string. Describes the # The linear alignment for this alignment record. This field is null for
# unmapped reads.
# mapped position and local alignment of the read to the reference.
@@ -327,12 +322,17 @@
# Specifically, this is -10 log10 Pr(mapping position is wrong), rounded to
# the nearest integer.
},
- "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.
+ "nextMatePosition": { # An abstraction for referring to a genomic position, in relation to some # The mapping of the primary alignment of the
+ # `(readNumber+1)%numberReads` read in the fragment. It replaces
+ # mate position and mate strand in SAM.
+ # 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.
+ "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.
+ },
},
],
}</pre>