I used the function blocklist_startend with type=snp and type=bp, and combined them in the table below
After the parallel window size (10000), the block has bp information, but not before.
Also, block 77 has no bp information, maybe because the block is inside the 1000 overlap size?
Hi again,
testing the new version HaploBlocker_1.6.02 RandomFieldsUtils_0.6.6
The first parallel window snps have no bp information
I called using Rscript parallel window 10000, overlap 1000
pwn=10000 won=1000
blocklist<-block_calculation(paste0(invcf,".vcf.gz"),adaptive_mode=TRUE,big_output=TRUE,overlap_remove=FALSE,window_cores=12,parallel_window=pwn,window_overlap=won)
I used the function blocklist_startend with type=snp and type=bp, and combined them in the table below
After the parallel window size (10000), the block has bp information, but not before. Also, block 77 has no bp information, maybe because the block is inside the 1000 overlap size?
[omitted first 58 rows]
block 59 7914 10356 0 0 block 60 7969 9620 0 0 block 61 8220 8715 0 0 block 62 8220 8766 0 0 block 63 8768 9608 0 0 block 64 9023 9608 0 0 block 65 9659 11000 0 0 block 66 9743 10560 0 0 block 67 9745 10338 0 0 block 68 9844 10219 0 0 block 69 10001 11771 1206576 1780371 block 70 10001 13357 1206576 1963559 block 71 10338 12260 1233753 1852355 block 72 10338 14851 1233753 2404501 block 73 10338 18800 1233753 3864793 block 74 10393 12786 1249255 1886914 block 75 10393 11906 1249255 1818989 block 76 10393 11294 1249255 1737954 block 77 10396 11000 0 0 block 78 10401 11052 1249466 1444048 block 79 11238 17824 1720428 3611249 block 80 11288 16434 1722229 2743049 block 81 11429 11801 1740848 1805056
Thanks
Matt