Strange sa_intervals found in kmer.precalc for toy example about gramtools

[iqbal-lab]

OK, @coelias , @sm0179 - I'm looking into this. The code loads up into the kmer hash precisely the intervals found by bidir_search_bwd(), so I'm stepping through that to see why it thinks (19,22) is there

[iqbal-lab]

Just logging this for digestion later. If I delete the precalc file , and run, then I notice that as it is going through bidir_search_bwd, the range search returns (21,5). I don't see how row 21 could ever be associated with 5

[iqbal-lab]

Some more toy stuff:

PRG = A5C6G5T
use kmer 2

This is the kmer file
AC
CT
AG
GT
which is correct

and this is the precalc file
3 4 |0|3 4 |7 9 |5 @|
1 3 |0|1 2 |6 8 |5 2 @|
2 4 |0|2 3 |6 8 |5 @|
1 2 |0|1 2 |6 6 |5 1 @|

Notice it marks all the kmers as not in ref (marked by the |0|). This is a bit confusing.
What kmers_in_ref means under the hood is, it does NOT have a match that is directly to the right of a number. That is true for all of these kmers.

So look at the first row
3 4 |0|3 4 |7 9 |5 @|

kmer GT has SA interval [3,4) - ie just the row 3.

bwm of A5C6G5T$ is
$A5C6G5T
5C6G5T$A
5T$A5C6G
6G5T$A5C
A5C6G5T$
C6G5T$A5
G5T$A5C6
T$A5C6G5

So that is right.

But now look at the second line
1 3 |0|1 2 |6 8 |5 2 @|

kmer AG has interval [1,2) - ie this line 5C6G5T$A - makes no sense
(The site info is right - it overlaps site 5 on allele 2)

Another error - final line:

1 2 |0|1 2 |6 6 |5 1 @|

kmer AC has interval [1,2) - ie row 1, ie 5C6G5T$A - again makes no sense

[iqbal-lab]

For the record, the SA intervals generated are correct for a PRG with no variation:

PRG: AACGTT

kmers file

AA
AC
CG
GT
TT

precalc file

4 4 |1|6 7 |6 9 ||
3 4 |1|4 5 |5 8 ||
2 3 |1|3 4 |4 7 ||
1 2 |1|2 3 |3 6 ||
1 1 |1|1 2 |2 5 ||

which is all consistent with this BWM

$AACGTT
AACGTT$
ACGTT$A
CGTT$AA
GTT$AAC <<<<<<
T$AACGT
TT$AACG

eg look at 2nd line: 34=GT and this is there on line indexed number 4, marked <<< above
So SA interval is [4,5)

[iqbal-lab]

Actually the fastest way to see there is a problem is to look at this

3 4 |0|3 4 |7 9 |5 @|
1 3 |0|1 2 |6 8 |5 2 @|
2 4 |0|2 3 |6 8 |5 @|
1 2 |0|1 2 |6 6 |5 1 @|

both the kmers AG and AC have the same SA interval = [1,2). Must be impossible.

PRG is A5C6G5T

bwm of A5C6G5T is
5C6G5TA
5TA5C6G
6G5TA5C
A5C6G5T
C6G5TA5
G5TA5C6
TA5C6G5

bwm of A5C6G5T$ is
$A5C6G5T
5C6G5T$A
5T$A5C6G
6G5T$A5C
A5C6G5T$
C6G5T$A5
G5T$A5C6
T$A5C6G5

[iqbal-lab]

Hm - so this is all a mess as I was generating those BWMs during debugging without converting to integers. Will close this and create a new clean one

[iqbal-lab]

Close this - is a mess. Open a new clean one.