Buffer bug???

[leedchou]

Hi,

I was trying different window and buffer parameters, getting weird results. When I run chunk with window-cm and window-mb less equal 1, whatever buffer-cm and buffer-mb is, buffer is always like +- 1,000,000bp based on window size. Below is an example:

0	chr1	chr1:1-2000069	chr1:1-1000066	1	1000003	33883	33471
1	chr1	chr1:51-3000098	chr1:1000067-2000088	1	1000005	55170	54534
2	chr1	chr1:1000079-4000121	chr1:2000089-3000102	1.00001	1000006	57783	56823
3	chr1	chr1:2000106-5000130	chr1:3000103-4000146	1.00001	1000014	54423	53362
4	chr1	chr1:3000172-6000191	chr1:4000147-5000194	1.00002	1000019	50088	49094

Moreover, it caused errors when running ligate like:
�[31mERROR: �[0mThree files overlapping at position: 1005908

Is that a bug?

Best regards,
Leed

[datngu]

Hi,
I have the same issue. Do you know the solution to avoid this error?

Best,
Dat

[LouisLeNezet]

I'm struggling with the same error on a small dataset.
This error is not present in GLIMPSE version1.
Here is some code to replicate the error.

wget https://raw.githubusercontent.com/nf-core/test-datasets/phaseimpute/hum_data/panel/chr21/1000GP.chr21.s.norel.vcf.gz
wget https://raw.githubusercontent.com/nf-core/test-datasets/phaseimpute/hum_data/panel/chr21/1000GP.chr21.s.norel.vcf.gz.csi

GLIMPSE_chunk \
        --input 1000GP.chr21.s.norel.vcf.gz --region chr21:16570000-16610000 \
        --window-size 10000 --window-count 400 --buffer-size 1000 --buffer-count 30 \
        --output test_chunks.txt # Give +buffer:[chr21:16570070-16592229] and +buffer:[chr21:16588251-16609998]

GLIMPSE2_chunk \
        --input 1000GP.chr21.s.norel.vcf.gz --region chr21:16570000-16610000 \
        --sequential --window-mb 0.01 --window-cm 0.01 --window-count 400 --buffer-mb 0.001 --buffer-cm 0.001 --buffer-count 30 \
        --output test_chunks.txt # Give Segmentation fault

GLIMPSE2_chunk \
        --input 1000GP.chr21.s.norel.vcf.gz --region chr21:16570000-16610000 \
        --sequential --window-mb 0.01 --window-cm 0.01 --window-count 200 --buffer-mb 0.001 --buffer-cm 0.001 --buffer-count 30 \
        --output test_chunks.txt # Give +buffer:[chr21:16570070-16609998] and +buffer:[chr21:16570070-16609998]