append error (bug?) #25
Description
I am running into an issue with append that results in either a core dump or a faulty getctg.
I am using this agc provided by @lh3 https://github.com/lh3/OpenHGL. To this agc (human579.agc) I am attempting to append two genomes (2 haplotypes of an assembly), HG02554.1.chr.fasta and HG02554.2.chr.fasta. If I try to append them both (as below) I get a core dump:
#this core dumps
~/local_modules_sw/agc-3.2_x64_linux/agc append human579.agc input/HG02554.1.chr.fasta input/HG02554.2.chr.fasta >./test/human579_plusHG02554.agc
3198569 Segmentation fault (core dumped)
I CAN append EITHER single genome without a core dump - however, if I then try to getctg I get strange behavior. For example - this fetch returns nothing:
~/local_modules_sw/agc-3.2_x64_linux/agc getctg ./test/human579_plusHG02554.1.agc [email protected]:145315365-146249433
>NC_060928.1 HG02554.1:145315365-146249433
I have created a reproducible example of this where I extracted the first 10Mb of HG02554.1.chr.fasta and try to append it to the agc. You can see that only the first 3350706 bases are able to be extracted from the agc.
wget https://raw.githubusercontent.com/petersudmant/agc_bugfix/refs/heads/main/HG02554.1_10M.chr.fasta
wc HG02554.1_10M.chr.fasta
#add to agc
~/local_modules_sw/agc-3.2_x64_linux/agc append human579.agc HG02554.1_10M.chr.fasta >./test/human579_plus_10M.agc
#fetch it
~/local_modules_sw/agc-3.2_x64_linux/agc getctg ./test/human579_plus_10M.agc NC_060928.1:[email protected]_10M.chr:1-10000000 | wc
Thanks!