Documentation

A nucleotide base. We only represent A,C,G,T. The contained Word8 ist guaranteed to be 0..3.

A nucleotide base in an alignment. Experience says we're dealing with Ns and gaps all the type, so purity be damned, they are included as if they were real bases.

To allow Nucleotidess to be unpacked and incorporated into containers, we choose to represent them the same way as the BAM file format: as a 4 bit wide field. Gaps are encoded as 0 where they make sense, N is 15. The contained Word8 is guaranteed to be 0..15.

Qualities are stored in deciban, also known as the Phred scale. To represent a value p, we store -10 * log_10 p. Operations work directly on the "Phred" value, as the name suggests. The same goes for the Ord instance: greater quality means higher "Phred" score, meand lower error probability.

A positive floating point value stored in log domain. We store the natural logarithm (makes computation easier), but allow conversions to the familiar "Phred" scale used for Qual values.

Common way of using Prob'.

Converts a character into a Nucleotides. The usual codes for A,C,G,T and U are understood, - and . become gaps and everything else is an N.

Converts a character into a Nucleotides. The usual codes for A,C,G,T and U are understood, - and . become gaps and everything else is an N.

Tests if a Nucleotides is a gap. Returns true only for the gap.

Tests if a Nucleotides is a base. Returns True for everything but gaps.

Tests if a Nucleotides is a proper base. Returns True for A,C,G,T only.

Complements a Nucleotides.

Complements a Nucleotides.

Sequence identifiers are ASCII strings Since we tend to store them for a while, we use strict byte strings.

Coordinates in a genome. The position is zero-based, no questions about it. Think of the position as pointing to the crack between two bases: looking forward you see the next base to the right, looking in the reverse direction you see the complement of the first base to the left.

To encode the strand, we (virtually) reverse-complement any sequence and prepend it to the normal one. That way, reversed coordinates have a negative sign and automatically make sense. Position 0 could either be the beginning of the sequence or the end on the reverse strand... that ambiguity shouldn't really matter.

Moves a Position. The position is moved forward according to the strand, negative indexes move backward accordingly.

Ranges in genomes We combine a position with a length. In 'Range pos len', pos is always the start of a stretch of length len. Positions therefore move in the opposite direction on the reverse strand. To get the same stretch on the reverse strand, shift r_pos by r_length, then reverse direction (or call reverseRange).

Moves a Range. This is just shiftPosition lifted.

Reverses a Range to give the same Range on the opposite strand.

Extends a range. The length of the range is simply increased.

Expands a subrange. (range1 insideRange range2) interprets range1 as a subrange of range2 and computes its absolute coordinates. The sequence name of range1 is ignored.

Wraps a range to a region. This simply normalizes the start position to be in the interval '[0,n)', which only makes sense if the Range is to be mapped onto a circular genome. This works on both strands and the strand information is retained.

Finds a file by searching the environment variable BIOHAZARD like a PATH.