locateVariants() and predictCoding() silently drop large INDELs

Tái hiện trường hợp này với rowRanges(vcf), locateVariants() và predictCoding() bằng VCF chứa INDEL lớn được cung cấp, đồng thời xác nhận biến thể biến mất ở đâu. Theo dõi các điểm vào đó để xác định cách xử lý hiện tại đối với các trình tự REF dài; công việc được xem là hoàn tất khi biến thể được giữ lại hoặc một cảnh báo/lỗi báo rõ ràng rằng biến thể đã bị loại bỏ, với độ bao phủ cho cả hai kết quả.

I have encountered an issue with large INDELs being silently discarded from my results.

This is the offending VCF entry:
contig_xyz 133527 Sniffles2.DEL.50S0 GGATGAACTCTTGGATTCTTGGGCTCATGTCGGACAGGATGCCGCCCCAGCTTCTCAGGTTGATGCCCTGGGATCTAGAATCCAGCAGTGTGGGCAGCACCCGGAACAGCTTGAAGAAGTCCACGTTGGCGTACAGGGTATCCTCGATCCACTGCAGGGTTCCCTGGCTCAGACTGCACAGGGCATATCTGACGGTCTTGGCGCCTCTCCGCTGGCTGAAGATGATGAACCGTTCCAGCAGGGCCTCAGAACAGGCGATATCCTTCAGGGCGAGATCTGGCACGCCATGAGCAAACTGCTCGGGCCGCACTTGGCTGTTGATCAGCAGGTACACCACGCTGTCGCTCAGGCCGATGTTCTTGATGAGGAACAGTGTCAGGGTTTCCTCGTCCTTCAGGATGTCCCGGATTCTGATGCCCCTGCCGGCGATTCTCTCGGGGTGTGTTCTCAGGGTGTCCATGAACTGGCTCAGGATGTGCAGCTCGGTCCAGATTCTGCCCAGGTGCTGAGACTCAGGGGCGTTCATCAGCAGCTCTTGGAAGTCCCGGTACACTCTGGCCAGGATGCTGTTGTTGTAGTTGGACACGATGCCAGGGCTTTCGCCAGGTGTGGGGCTCTGAAAGCAGGGGTTGTTCACGTTGCAGAAGATGCCCTGCAGCCAAGGCAGCATTCCGGCAGAAGGCATGGCCTTGTTGGGGAAGTGACACTCGTGGTGGCTGTACAGAGGATTGGCGTTCCGCAGCCAGATCAGCACCAGAAACAGGCTCAGGGGCCACACGAGTTCCACCACGAATCTGATTTTCTGCCGCTTCCGCAGGGTCCAGTTCTTCCACAGCAGCAGCTGAATCTGCCGCACGAATCCCATGGTGGCCAGCTCGGTCGTCCCGGGGCCTCTACTGTCCAGAGTCCTCCGCGGATCCCGATCTGACGGTTCACTAAACGAGCTCTGTTTATATAGACCTCCCACCGTACACGCCTACCGCCCATTTGCGTCAACGGGGCGGGCGATCGCAGTTGTTACGACATTTTGGAAAGTCCCGTTGATTTTGGTGCCAAAACAAACTCCCATTGACGTCAATGGGGTGGAGACTTGGAAATCCCCGTGAGTCAAACCGCTATCCACGCCCATTGGTGTACTGCCAAAACCGCATCACCATGGTAATAGCGATGACTAATACGTAGATGTACTGCCAAGTAGGAAAGTCCCGTAAGGTCATGTACTGGGCATAATGCCAGGCGGGCCATTTACCGTCATTGACGTCAATAGGGGGCGGACTTGGCATATGATACACTTGATGTACTGCCAAGTGGGCAGTTTACCGTAAATACTCCACCCATTGACGTCAATGGAAAGTCCCTATTGGCGTTACTATGGGAACATACGTCATTATTGACGTCAATGGGCGGGGGTCGTTGGGCGGTCAGCCAGGCGGGCCATTTACCGTAAGTTATGTAACGCGGAACTCCATATATGGGCTATGAACTAATGACCCCGTAATTGATTACTATTAATAACTAGTCAATAATCAATGCCAACATGGCGGTCATATTGGACATGAGCCAATATAAATGTACATATTATGATATAGATACAACGTATGCAATGGCCAATAGCCAATATTGATTTATGCTATATAACCAATGAATAATATGGCTAATGGCCAATATTGAAGATCCCCGGGTACCGAGCTCGAATTCATCGATGATGATCCACTAGTAACGGCCGCCAGTGTGCTGGAATTCGCCCTTCCCGCATGGCATCTCATTACCGCCCGATCCGGCGGTTTCCGCTTCCGTTCCGCATGCTAACGAGGAACGGGCAGGGGGCGGGGCCCGGGCCCCGACTTCCCGGTTCGGCGGTAATGTGATACGAGCCCCGCGCGCCCGTTGGCCGTCCCCGGGCCCCCGGTCCCGCCCGCCGGACGCCGGGACCAACGGGACGGCGGGCGGCCCTTGGGCCGCCCGCCTTGCCGCCCCCCCATTGGCCGGCGGGCGGGACCGCCCCAAGGGGGCGGGGCCGCCGGGTAAAAGAAGTGAGAACGCGAAGCGTTCGCACTTCGTCCCAATATATATATATTATTAGGGCGAAGTGCGAGCACTGGCGCCGTGCCCGACTCCGCGCCGGCCCCGGGGGCGGACCCGGGCGGCGGGGGGCGGGTCTCTCCGGCGCACATAAAGGCCCGGCGCGACCGACGCCCGCAGACGGCGCCGGCCACGAACGACGGGAGCGGCTGCGGAGCACGCGGACCGGGAGCGGGAGTCGCAGAGGGCCGTCGGAGCGGACGGCGTCGGCATCGCGACGCCCCGGCTCGGGATCGGGATCGCATCGGAAAGGGACACGCGGACGCGGGGGGGAAAGACCCGCCCACCCCACCCACGAAACACAGGGGACGCACCCCGGGGGCCTCCGACGACAGAAACCCACCGGTCCGCCTTTTTTGCACGGGTAAGCACCTTGGGTGGGCGGAGGAGGGGGGACGCGGGGGCGGAGGAGGGGGGACGCGGGGGCCGGAGGAGGGGGGACGCGGGGGCGGAGGAGGGGG G 59 PASS PRECISE;SVTYPE=DEL;SVLEN=-2542;END=136069;SUPPORT=259;COVERAGE=335,326,308,260,257;STRAND=+-;AF=0.869;STDEV_LEN=0;STDEV_POS=0 GT:GQ:DR:DV 1/1:60:39:259

This represents a deletion of 2542 bp.

The large deletion is present when I call
rowRanges(vcf)

So it is successfully being read by readVcf()

However, when I call:

locateVariants(
  vcf,
  txdb,
  AllVariants(
    promoter = PromoterVariants(0,0),
    intergenic = IntergenicVariants(0,0)
    )
  )

or
predictCoding(vcf, txdb, seqSource=fasta)

this variant position is not included among the results.

With some trial and error, I have determined that truncating the REF sequence to 800 characters allows the variant to be maintained, but 850 characters fails.

Success, 850 bp
contig_xyz 133527 Sniffles2.DEL.50S0 GGATGAACTCTTGGATTCTTGGGCTCATGTCGGACAGGATGCCGCCCCAGCTTCTCAGGTTGATGCCCTGGGATCTAGAATCCAGCAGTGTGGGCAGCACCCGGAACAGCTTGAAGAAGTCCACGTTGGCGTACAGGGTATCCTCGATCCACTGCAGGGTTCCCTGGCTCAGACTGCACAGGGCATATCTGACGGTCTTGGCGCCTCTCCGCTGGCTGAAGATGATGAACCGTTCCAGCAGGGCCTCAGAACAGGCGATATCCTTCAGGGCGAGATCTGGCACGCCATGAGCAAACTGCTCGGGCCGCACTTGGCTGTTGATCAGCAGGTACACCACGCTGTCGCTCAGGCCGATGTTCTTGATGAGGAACAGTGTCAGGGTTTCCTCGTCCTTCAGGATGTCCCGGATTCTGATGCCCCTGCCGGCGATTCTCTCGGGGTGTGTTCTCAGGGTGTCCATGAACTGGCTCAGGATGTGCAGCTCGGTCCAGATTCTGCCCAGGTGCTGAGACTCAGGGGCGTTCATCAGCAGCTCTTGGAAGTCCCGGTACACTCTGGCCAGGATGCTGTTGTTGTAGTTGGACACGATGCCAGGGCTTTCGCCAGGTGTGGGGCTCTGAAAGCAGGGGTTGTTCACGTTGCAGAAGATGCCCTGCAGCCAAGGCAGCATTCCGGCAGAAGGCATGGCCTTGTTGGGGAAGTGACACTCGTGGTGGCTGTACAGAGGATTGGCGTTCCGCAGCCAGATCAGCACCAGAAACAGGCTCAGGGGCCACACGAGTTCCACCACGAATCTGATTTTCTGCCGCTTCCGCAGGGTCCAGTTCTTCCACAGCAGCAGCTGAATCTG G 59 PASS PRECISE;SVTYPE=DEL;SVLEN=-2542;END=136069;SUPPORT=259;COVERAGE=335,326,308,260,257;STRAND=+-;AF=0.869;STDEV_LEN=0;STDEV_POS=0 GT:GQ:DR:DV 1/1:60:39:259

Fails, 900 bp
contig_xyz 133527 Sniffles2.DEL.50S0 GGATGAACTCTTGGATTCTTGGGCTCATGTCGGACAGGATGCCGCCCCAGCTTCTCAGGTTGATGCCCTGGGATCTAGAATCCAGCAGTGTGGGCAGCACCCGGAACAGCTTGAAGAAGTCCACGTTGGCGTACAGGGTATCCTCGATCCACTGCAGGGTTCCCTGGCTCAGACTGCACAGGGCATATCTGACGGTCTTGGCGCCTCTCCGCTGGCTGAAGATGATGAACCGTTCCAGCAGGGCCTCAGAACAGGCGATATCCTTCAGGGCGAGATCTGGCACGCCATGAGCAAACTGCTCGGGCCGCACTTGGCTGTTGATCAGCAGGTACACCACGCTGTCGCTCAGGCCGATGTTCTTGATGAGGAACAGTGTCAGGGTTTCCTCGTCCTTCAGGATGTCCCGGATTCTGATGCCCCTGCCGGCGATTCTCTCGGGGTGTGTTCTCAGGGTGTCCATGAACTGGCTCAGGATGTGCAGCTCGGTCCAGATTCTGCCCAGGTGCTGAGACTCAGGGGCGTTCATCAGCAGCTCTTGGAAGTCCCGGTACACTCTGGCCAGGATGCTGTTGTTGTAGTTGGACACGATGCCAGGGCTTTCGCCAGGTGTGGGGCTCTGAAAGCAGGGGTTGTTCACGTTGCAGAAGATGCCCTGCAGCCAAGGCAGCATTCCGGCAGAAGGCATGGCCTTGTTGGGGAAGTGACACTCGTGGTGGCTGTACAGAGGATTGGCGTTCCGCAGCCAGATCAGCACCAGAAACAGGCTCAGGGGCCACACGAGTTCCACCACGAATCTGATTTTCTGCCGCTTCCGCAGGGTCCAGTTCTTCCACAGCAGCAGCTGAATCTGCCGCACGAATCCCATGGTGGCCAGCTCGGTCGTCCCGGGGCCTCTACTGT G 59 PASS PRECISE;SVTYPE=DEL;SVLEN=-2542;END=136069;SUPPORT=259;COVERAGE=335,326,308,260,257;STRAND=+-;AF=0.869;STDEV_LEN=0;STDEV_POS=0 GT:GQ:DR:DV 1/1:60:39:259

Can you suggest a way to maintain these large INDELs among the results?
Alternatively, if it is impossible to maintain large INDELs, could a warning or error be returned instead of a silent discard?

Thanks!