Safe Haskell  None 

Language  Haskell98 
 data PrimChunks
 = Seek Int PrimBase
  Indel [Nucleotides] [DamagedBase] PrimBase
  EndOfRead
 data PrimBase = Base {
 _pb_wait :: Int
 _pb_likes :: DamagedBase
 _pb_mapq :: Qual
 _pb_rev :: Bool
 _pb_chunks :: PrimChunks
 type PosPrimChunks = (Refseq, Int, PrimChunks)
 data DamagedBase = DB {
 db_call :: !Nucleotide
 db_qual :: !Qual
 db_ref :: !Nucleotides
 db_dmg :: !Mat44D
 decompose :: [Mat44D] > BamRaw > Maybe PosPrimChunks
 data CallStats = CallStats {
 read_depth :: !Int
 reads_mapq0 :: !Int
 sum_mapq :: !Int
 sum_mapq_squared :: !Int
 type GL = Vector Prob
 newtype V_Nuc = V_Nuc (Vector Nucleotide)
 newtype V_Nucs = V_Nucs (Vector Nucleotides)
 data IndelVariant = IndelVariant {
 deleted_bases :: !V_Nucs
 inserted_bases :: !V_Nuc
 type BasePile = [(Qual, DamagedBase)]
 type IndelPile = [(Qual, ([Nucleotides], [DamagedBase]))]
 data Pile' a b = Pile {
 p_refseq :: !Refseq
 p_pos :: !Int
 p_snp_stat :: !CallStats
 p_snp_pile :: a
 p_indel_stat :: !CallStats
 p_indel_pile :: b
 type Pile = Pile' (BasePile, BasePile) IndelPile
 pileup :: Monad m => Enumeratee [PosPrimChunks] [Pile] m a
 newtype PileM m a = PileM {}
 type PileF m r = Refseq > Int > [PrimBase] > Heap > (Stream [Pile] > Iteratee [Pile] m r) > Stream [PosPrimChunks] > Iteratee [PosPrimChunks] m (Iteratee [Pile] m r)
 get_refseq :: PileM m Refseq
 get_pos :: PileM m Int
 upd_pos :: (Int > Int) > PileM m ()
 set_pos :: (Refseq, Int) > PileM m ()
 get_active :: PileM m [PrimBase]
 upd_active :: ([PrimBase] > [PrimBase]) > PileM m ()
 add_active :: PrimBase > PileM m ()
 clr_active :: PileM m [PrimBase]
 ins_waiting :: Int > PrimBase > PileM m ()
 get_waiting :: PileM m Heap
 set_waiting :: Heap > PileM m ()
 yield :: Monad m => Pile > PileM m ()
 peek :: PileM m (Maybe PosPrimChunks)
 bump :: PileM m ()
 consume_active :: a > (a > PrimBase > PileM m a) > PileM m a
 pileup' :: Monad m => PileM m ()
 pileup'' :: Monad m => PileM m ()
 p'feed_input :: PileM m ()
 p'check_waiting :: PileM m ()
 p'scan_active :: PileM m ((CallStats, [(Qual, Either DamagedBase DamagedBase)]), (CallStats, [(Qual, ([Nucleotides], [DamagedBase]))]))
 partitionPairEithers :: [(a, Either b c)] > ([(a, b)], [(a, c)])
 data Heap
 union :: Heap > Heap > Heap
 getMinKey :: Heap > Maybe Int
 viewMin :: Heap > Maybe (Int, PrimBase, Heap)
TODO*
A whole lot of testing.
ML fitting and evaluation of parameters for different possible
Maybe specialize to ploidy one and two.
data PrimChunks Source
The primitive pieces for genotype calling: A position, a base represented as four likelihoods, an inserted sequence, and the length of a deleted sequence. The logic is that we look at a base followed by some indel, and all those indels are combined into a single insertion and a single deletion.
Seek Int PrimBase  skip to position (at start or after N operation) 
Indel [Nucleotides] [DamagedBase] PrimBase  observed deletion and insertion between two bases 
EndOfRead  nothing anymore 
Base  more chunks 

type PosPrimChunks = (Refseq, Int, PrimChunks) Source
data DamagedBase Source
Represents our knowledge about a certain base, which consists of the base itself (A,C,G,T, encoded as 0..3; no Ns), the quality score (anything that isn't A,C,G,T becomes A with quality 0), and a substitution matrix representing postmortem but presequencing substitutions.
Unfortunately, none of this can be rolled into something more simple, because damage and sequencing error behave so differently.
DB  damage matrix 

decompose :: [Mat44D] > BamRaw > Maybe PosPrimChunks Source
Decomposes a BAM record into chunks suitable for piling up. We pick apart the CIGAR and MD fields, and combine them with sequence and quality as appropriate. Clipped bases are removed/skipped as appropriate. We also do apply a substitution matrix to each base, which must be supplied along with the read.
Statistics about a genotype call. Probably only useful for fitlering (so not very useful), but we keep them because it's easy to track them.
CallStats  

Genotype likelihood values. A variant call consists of a position,
some measure of qualities, genotype likelihood values, and a
representation of variants. A note about the GL values: VCF
would
normalize them so that the smallest one becomes zero. We do not do
that here, since we might want to compare raw values for a model
test. We also store them in a Double
to make arithmetics easier.
Normalization is appropriate when converting to VCF
.
If GL is given, we follow the same order used in VCF: "the ordering of genotypes for the likelihoods is given by: F(jk) = (k*(k+1)2)+j. In other words, for biallelic sites the ordering is: AA,AB,BB; for triallelic sites the ordering is: AA,AB,BB,AC,BC,CC, etc."
data IndelVariant Source
type BasePile = [(Qual, DamagedBase)] Source
Map quality and a list of encountered bases, with damage information and reference base if known.
type IndelPile = [(Qual, ([Nucleotides], [DamagedBase]))] Source
Map quality and a list of encountered indel variants. The deletion has the reference sequence, if known, an insertion has the inserted sequence with damage information.
Running pileup results in a series of piles. A Pile
has the
basic statistics of a VarCall
, but no GL values and a pristine list
of variants instead of a proper call. We emit one pile with two
BasePile
s (one for each strand) and one IndelPile
(the one
immediately following) at a time.
Pile  

pileup :: Monad m => Enumeratee [PosPrimChunks] [Pile] m a Source
The pileup enumeratee takes BamRaw
s, decomposes them, interleaves
the pieces appropriately, and generates Pile
s. The output will
contain at most one BasePile
and one IndelPile
for each position,
piles are sorted by position.
This top level driver receives BamRaw
s. Unaligned reads and
duplicates are skipped (but not those merely failing quality checks).
Processing stops when the first read with invalid br_rname
is
encountered or a t end of file.
The pileup logic keeps a current coordinate (just two integers) and
two running queues: one of active PrimBase
s that contribute to
current genotype calling and on of waiting PrimBase
s that will
contribute at a later point.
Oppan continuation passing style! Not only is the CPS version of the
state monad (we have five distinct pieces of state) somewhat faster,
we also need CPS to interact with the mechanisms of Iteratee
. It
makes implementing yield
, peek
, and bump
straight forward.
type PileF m r = Refseq > Int > [PrimBase] > Heap > (Stream [Pile] > Iteratee [Pile] m r) > Stream [PosPrimChunks] > Iteratee [PosPrimChunks] m (Iteratee [Pile] m r) Source
The things we drag along in PileM
. Notes:
* The active queue is a simple stack. We add at the front when we
encounter reads, which reverses them. When traversing it, we traverse
reads backwards, but since we accumulate the BasePile
, it gets reversed
back. The new active queue, however, is no longer reversed (as it should
be). So after the traversal, we reverse it again. (Yes, it is harder to
understand than using a proper deque type, but it is cheaper.
There may not be much point in the reversing, though.)
get_refseq :: PileM m Refseq Source
get_active :: PileM m [PrimBase] Source
upd_active :: ([PrimBase] > [PrimBase]) > PileM m () Source
add_active :: PrimBase > PileM m () Source
clr_active :: PileM m [PrimBase] Source
ins_waiting :: Int > PrimBase > PileM m () Source
get_waiting :: PileM m Heap Source
set_waiting :: Heap > PileM m () Source
yield :: Monad m => Pile > PileM m () Source
Sends one piece of output downstream. You are not expected to understand how this works, but at last it doesn't leak memory.
peek :: PileM m (Maybe PosPrimChunks) Source
Inspect next input element, if any. Returns Just b
if b
is the
next input element, Nothing
if no such element exists. Waits for
more input if nothing is available immediately.
Discard next input element, if any. Does nothing if input has already ended. Waits for input to discard if nothing is available immediately.
consume_active :: a > (a > PrimBase > PileM m a) > PileM m a Source
pileup' :: Monad m => PileM m () Source
The actual pileup algorithm. If active contains something, continue here. Else find the coordinate to continue from, which is the minimum of the next waiting coordinate and the next coordinate in input; if found, continue there, else we're all done.
p'feed_input :: PileM m () Source
Feeds input as long as it starts at the current position
p'check_waiting :: PileM m () Source
Checks waiting queue. If there is anything waiting for the current position, moves it to active queue.
p'scan_active :: PileM m ((CallStats, [(Qual, Either DamagedBase DamagedBase)]), (CallStats, [(Qual, ([Nucleotides], [DamagedBase]))])) Source
partitionPairEithers :: [(a, Either b c)] > ([(a, b)], [(a, c)]) Source