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License: MIT License
Convert structural variants to sequence graphs [ VCF + FASTA ---> GFA ]
License: MIT License
Hello,
would it be possible to have svaha available as a anaconda package?
Thank you in advance!
Andrea
svaha doesn't support flat alleles, which we use for variant recall in vg right now. It would be nice to have it as an option, even if the new SnarlTraversal-based variant pipeline should remove our dependencies on nice, flat alleles.
GFAKluge itself needs updates, and then we need to update svaha to handle said updates as we move vg to gfa2.
When inserting a SNP and an SV into the graph the two variants may not share a start position. This is because of the way we do indexing. We also have the problem that SNP IDs are non-contiguous in the graph and break the monotonic increasing nature of SV IDs. Further, SNPs currently can't start a contig graph.
/usr/bin/ld: libhts.a(rANS_static.o): relocation R_X86_64_32 against .rodata' can not be used when making a PIE object; recompile with -fPIE /usr/bin/ld: libhts.a(thread_pool.o): relocation R_X86_64_32 against
.text' can not be used when making a PIE object; recompile with -fPIE
/usr/bin/ld: libhts.a(vlen.o): relocation R_X86_64_32S against .rodata' can not be used when making a PIE object; recompile with -fPIE /usr/bin/ld: libhts.a(zfio.o): relocation R_X86_64_32 against
.rodata.str1.1' can not be used when making a PIE object; recompile with -fPIE
/usr/bin/ld: libhts.a(knetfile.o): relocation R_X86_64_32 against .rodata.str1.1' can not be used when making a PIE object; recompile with -fPIE /usr/bin/ld: libhts.a(md5.o): relocation R_X86_64_32S against
.rodata.str1.1' can not be used when making a PIE object; recompile with -fPIE
/usr/bin/ld: libhts.a(sam.o): relocation R_X86_64_32 against .rodata.str1.8' can not be used when making a PIE object; recompile with -fPIE /usr/bin/ld: libhts.a(files.o): relocation R_X86_64_PC32 against symbol
__xstat@@GLIBC_2.2.5' can not be used when making a PIE object; recompile with -fPIE
/usr/bin/ld: final link failed: bad value
collect2: error: ld returned 1 exit status
make[1]: *** [Makefile:294: bgzip] Error 1
make[1]: Leaving directory '/home/dnanexus/svaha/deps/htslib'
make: *** [Makefile:33: lib/libhts.a] Error 2
lasso uses the IDs as a map(basepair : node) in the graph. This unfortunately means that our ID space across multiple contigs quickly grows, and that there are collisions in the GFA output if we have multiple variant contigs (though we could construct each contig graph individually and then join them with a vg ids -j
).
We should ideally maintain our map outside of ID space and then increment IDs by one every time a new node is added. This is in line with what VG does.
Do I truncate the fasta, the vcf, or both?
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