Fields - sam_v1_6_alignment_qname :: ByteString
Query template NAME.
reads/segments having identical QNAME are regarded to come from
the same template. A QNAME ‘*’ indicates the information
is unavailable. In a SAM file, a read may
occupy multiple alignment lines, when its alignment is chimeric
or when multiple mappings are given. - sam_v1_6_alignment_flag :: Int
Combination of bitwise FLAGs. - sam_v1_6_alignment_rname :: ByteString
Reference sequence NAME of the alignment.
If @SQ header lines are present, RNAME (if not
‘*’) must be present in one of the SQ-SN tag.
An unmapped segment without coordinate has a ‘*’ at
this field. However, an unmapped segment may also have
an ordinary coordinate such that it can be
placed at a desired position after sorting.
If RNAME is ‘*’, no assumptions can be made about POS
and CIGAR. - sam_v1_6_alignment_pos :: Integer
1-based leftmost mapping POSition of the first CIGAR
operation that “consumes” a reference
base. The first base in a reference sequence has coordinate 1.
POS is set as 0 for an unmapped read without coordinate.
If POS is 0, no assumptions can be made about RNAME and CIGAR. - sam_v1_6_alignment_mapq :: Int
MAPping Quality. It equals −10 log10 Pr{mapping position is wrong},
rounded to the nearest integer. A value 255 indicates that the
mapping quality is not available. - sam_v1_6_alignment_cigar :: ByteString
CIGAR string (set ‘*’ if unavailable). - sam_v1_6_alignment_rnext :: ByteString
Reference sequence name of the primary alignment of the
NEXT read in the template. For the last read, the next read
is the first read in the template. If @SQ header lines are present,
RNEXT (if not ‘*’ or ‘=’) must be present in one of the SQ-SN tag.
This field is set as ‘*’ when the information is unavailable,
and set as ‘=’ if RNEXT is identical RNAME. If not ‘=’ and the next
read in the template has one primary mapping (see also bit 0x100 in FLAG),
this field is identical to RNAME at the primary line of the next read.
If RNEXT is ‘*’, no assumptions can be made on PNEXT and bit 0x20. - sam_v1_6_alignment_pnext :: Integer
1-based Position of the primary alignment of the NEXT read in
the template. Set as 0 when the information is unavailable.
This field equals POS at the primary line of the next read.
If PNEXT is 0, no assumptions can be made on RNEXT and bit 0x20. - sam_v1_6_alignment_tlen :: Integer
signed observed Template LENgth. For primary reads where the primary
alignments of all reads in the template are mapped to the same reference
sequence, the absolute value of TLEN equals the distance between the
mapped end of the template and the mapped start of the template,
inclusively (i.e., end − start + 1).
Note that mapped base is defined to be one that aligns to the
reference as described by CIGAR, hence excludes soft-clipped bases.
The TLEN field is positive for the leftmost segment of the template,
negative for the rightmost, and the sign for any middle segment is undefined.
If segments cover the same coordinates then the choice of which is leftmost
and rightmost is arbitrary, but the two ends must still have differing signs.
It is set as 0 for a single-segment template or when the information
is unavailable (e.g., when the first or last segment of a multi-segment
template is unmapped or when the two are mapped to
different reference sequences). - sam_v1_6_alignment_seq :: ByteString
segment SEQuence. This field can be a ‘*’ when the sequence
is not stored. If not a ‘*’, the length of the sequence must
equal the sum of lengths of MIS=X operations in CIGAR.
An ‘=’ denotes the base is identical to the reference base.
No assumptions can be made on the letter cases. - sam_v1_6_alignment_qual :: ByteString
ASCII of base QUALity plus 33 (same as the quality string
in the Sanger FASTQ format). A base quality is the phred-scaled
base error probability which equals −10 log10 Pr{base is wrong}.
This field can be a ‘*’ when quality is not stored.
If not a ‘*’, SEQ must not be a ‘*’ and the length of the quality
string ought to equal the length of SEQ. - sam_v1_6_alignment_optionalfields :: Maybe (Seq SAM_V1_6_Alignment_OptionalFields)
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