use malloc

[siebrenf]

C function pfmscan() will now store the intermediate scores in the heap (the RAM I think, this is my first tangle with C).

With my test FASTA, two arrays are created that are way bigger than the stack size. We could store these arrays on the heap, at the cost of speed. However, if the length of the sequences are normally not that large, we could also throw an error/warning instead.

Note: One thing that I could not get to work, is dynamically deciding to use the stack/heap (you cannot declare a variable inside an if-else in C, and then use it outside the if-else).

How to test:

Command line:

git clone [email protected]:vanheeringen-lab/gimmemotifs.git
cd gimmemotifs
git checkout option_1
python setup.py build && pip install .

Python:

from gimmemotifs.motif import Motif, read_motifs
from gimmemotifs.fasta import Fasta


jaspar_motif_file="data/motif_databases/JASPAR2022_vertebrates.pfm"
motifs = read_motifs(jaspar_motif_file)
print(len([m for m in motifs if m.id.startswith("MA0046.2")]))  # prints 1

m = [m for m in motifs if m.id.startswith("MA0046.2")][0]
print(m.id)  # prints 'MA0046.2_MA0046.2.HNF1A'

ff = "test/data/scan/genome/scan_test.fa"  # segfault

f = Fasta(ff)
m.scan_all(f)