VCF support for RLE and fix to same-as-reference allele normalization to RLE

[theferrit32]

Close #577
Close #587

[theferrit32]

Only thing left is addressing this comment
#589 (comment)

[korikuzma]

Submitting review for VCF code now. Going to be looking at the normalize fix next.

[korikuzma]

Tests LGTM

[theferrit32]

VCF changes after fixing the max seq limit logic, and bumping it up to 50bp to match the rle_seq_limit default elsewhere

vrs-python/src/ga4gh/vrs/normalize.py

Line 86 in 9462037

def _normalize_allele(input_allele, data_proxy, rle_seq_limit=50):

git diff --word-diff-regex='[^;]+' -- **/*.vcf

tests/extras/data/test_vcf_expected_altsonly_output.vcf
chr19 289464 . T TCACGCCTGTAATCC 50 PASS platforms=4;platformnames=Illumina,PacBio,CG,10X;datasets=4;datasetnames=HiSeqPE300x,CCS15kb_20kb,CGnormal,10XChromiumLR;callsets=6;callsetnames=HiSeqPE300xGATK,CCS15kb_20kbGATK4,CGnormal,HiSeqPE300xfreebayes,CCS15kb_20kbDV,10XLRGATK;datasetsmissingcall=IonExome,SolidSE75bp;callable=CS_HiSeqPE300xGATK_callable,CS_10XLRGATK_callable,CS_CCS15kb_20kbGATK4_callable,CS_CGnormal_callable,CS_HiSeqPE300xfreebayes_callable;filt=CS_CCS15kb_20kbDV_filt,CS_CCS15kb_20kbGATK4_filt;VRS_Allele_IDs=ga4gh:VA.ySvDptXfHB_9WEfu78v32DzBXJfwGgO7;VRS_Starts=289464;VRS_Ends=289466;[-VRS_States-]{+VRS_States=CACGCCTGTAATCCCA+};VRS_Lengths=.;VRS_RepeatSubunitLengths=. GT:PS:DP:ADALL:AD:GQ 0/1:.:518:94,98:116,137:785

tests/extras/data/test_vcf_expected_output.vcf
chr19 289464 . T TCACGCCTGTAATCC 50 PASS platforms=4;platformnames=Illumina,PacBio,CG,10X;datasets=4;datasetnames=HiSeqPE300x,CCS15kb_20kb,CGnormal,10XChromiumLR;callsets=6;callsetnames=HiSeqPE300xGATK,CCS15kb_20kbGATK4,CGnormal,HiSeqPE300xfreebayes,CCS15kb_20kbDV,10XLRGATK;datasetsmissingcall=IonExome,SolidSE75bp;callable=CS_HiSeqPE300xGATK_callable,CS_10XLRGATK_callable,CS_CCS15kb_20kbGATK4_callable,CS_CGnormal_callable,CS_HiSeqPE300xfreebayes_callable;filt=CS_CCS15kb_20kbDV_filt,CS_CCS15kb_20kbGATK4_filt;VRS_Allele_IDs=ga4gh:VA.nqqTUy-a2gssemOmJb4CJv-HNuFAmGrO,ga4gh:VA.ySvDptXfHB_9WEfu78v32DzBXJfwGgO7;VRS_Starts=289463,289464;VRS_Ends=289464,289466;[-VRS_States=T,-]{+VRS_States=T,CACGCCTGTAATCCCA+};VRS_Lengths=1,.;VRS_RepeatSubunitLengths=1,. GT:PS:DP:ADALL:AD:GQ 0/1:.:518:94,98:116,137:785

[korikuzma]

Fantastic work @theferrit32 🚀