Benchmark results in NoneType error

[archmageirvine]

Version : Truvari v3.4.0

Describe the bug :

Running a benchmark comparison between NIST NA24385 standard and output from a depth-based CNV caller results in a NoneType error. The following example is from output of the DRAGEN depth-based caller, but the same exception is observed on RTG segment outputs (but no exception is seen on CNVkit outputs). The exception occurs whether or not --pctsim=0 is used.

To Reproduce :

truvari bench -b hg002-truth/HG002_GRCh38_CMRG_SV_v1.00.vcf.gz -c dragen-cnv/NA24385.cnv.vcf.gz -f ../ref/38/Homo_sapiens_assembly38.fasta -o truvari-out2 --pctsim=0   
2022-08-17 02:30:12,354 [INFO] Running /home/sean/BIO-11269-xg-cnv-comparison/truvari/bin/truvari bench -b hg002-truth/HG002_GRCh38_CMRG_SV_v1.00.vcf.gz -c dragen-cnv/NA24385.cnv.vcf.gz -f ../ref/38/Homo_sapiens_assembly38.fasta -o truvari-out2 --pctsim=0
2022-08-17 02:30:12,354 [INFO] Params:
{
    "base": "hg002-truth/HG002_GRCh38_CMRG_SV_v1.00.vcf.gz",
    "comp": "dragen-cnv/NA24385.cnv.vcf.gz",
    "output": "truvari-out2",
    "reference": "../ref/38/Homo_sapiens_assembly38.fasta",
    "giabreport": false,
    "debug": false,
    "prog": false,
    "refdist": 500,
    "pctsim": 0.0,
    "minhaplen": 50,
    "pctsize": 0.7,
    "pctovl": 0.0,
    "typeignore": false,
    "use_lev": false,
    "chunksize": 1000,
    "gtcomp": false,
    "bSample": null,
    "cSample": null,
    "sizemin": 50,
    "sizefilt": 30,
    "sizemax": 50000,
    "passonly": false,
    "no_ref": false,
    "includebed": null,
    "extend": 0,
    "multimatch": false
}
2022-08-17 02:30:12,354 [INFO] Truvari version: 3.4.0
Traceback (most recent call last):
  File "/home/sean/BIO-11269-xg-cnv-comparison/truvari/bin/truvari", line 10, in <module>
    sys.exit(main())
  File "/home/sean/BIO-11269-xg-cnv-comparison/truvari/lib/python3.7/site-packages/truvari/__main__.py", line 85, in main
    TOOLS[args.cmd](args.options)
  File "/home/sean/BIO-11269-xg-cnv-comparison/truvari/lib/python3.7/site-packages/truvari/bench.py", line 799, in bench_main
    for call in itertools.chain.from_iterable(map(compare_chunk, chunks)):
  File "/home/sean/BIO-11269-xg-cnv-comparison/truvari/lib/python3.7/site-packages/truvari/bench.py", line 365, in chunker
    if not matcher.filter_call(entry, key == 'base'):
  File "/home/sean/BIO-11269-xg-cnv-comparison/truvari/lib/python3.7/site-packages/truvari/bench.py", line 157, in filter_call
    size = truvari.entry_size(entry)
  File "/home/sean/BIO-11269-xg-cnv-comparison/truvari/lib/python3.7/site-packages/truvari/comparisons.py", line 421, in entry_size
    elif entry.alts[0].count("<"):
TypeError: 'NoneType' object is not subscriptable

Expected behavior :

Maybe this kind of comparison is not supported by Truvari, but it would be nice to have a clearer message regarding the problem.

Example Data :

The data from the copy number caller are not sequence resolved, initial records:

#CHROM  POS     ID      REF     ALT     QUAL    FILTER  INFO    FORMAT  HG002_NA24385
chr1    818023  DRAGEN:REF:chr1:818023-1325928  N       .       51      PASS    END=1325928;REFLEN=507906       GT:SM:CN:BC:PE  ./.:1.05255:2:407:4,7
chr1    1325928 DRAGEN:GAIN:chr1:1325929-1342978        N       <DUP>   10      PASS    SVLEN=17050;SVTYPE=CNV;END=1342978;REFLEN=17050 GT:SM:CN:BC:PE  ./1:1.29637:3:17:7,11
chr1    1342979 DRAGEN:REF:chr1:1342979-2653404 N       .       66      PASS    END=2653404;REFLEN=1310426      GT:SM:CN:BC:PE  ./.:1.02852:2:1031:11,207
...

The benchmark is sequence resolved:

#CHROM  POS     ID      REF     ALT     QUAL    FILTER  INFO    FORMAT  HG002
chr1    1041776 .       CCGGCCAGTGCCAGGGTCGAGGTGGGCGGCTCCCCCGGGGGAGGGCTG        C       30      .       REPTYPE=CONTRAC;BREAKSIMLENGTH=143;REFWIDENED=chr1:1041679-1041868      GT:AD   1|1:0,2
chr1    23884345        .       T       TTAGAGGCGTGAGCCACTACACCTGGCTATGTATACTTTAGTGATTATTTTTCCTCAAAACATTAAATATTAAAACACTAAAGTAGTTACAATTGAAAAATTGAAAGTTAAGTGTATTAAAACTTAAAATATTACTTTACTATTATTATTTAAAATAGAGGCCGGATATGGTAGCTCACACCTATAATCCCAGCACTTTGGGAGGCCAACGCTGGCAGATCACTTGAGGTCAGGAGTTTGAGATCAGCCTGGCCAACATGGTGAAACCCAGTCTCTACTAAAAGTACAAAAAAAGAAAAAACAATTAGCTGAGAATGGTGGCTCATGTCCGTATTCCCAGCTATTCCAGAGTCTGAGGCACGAGAATCACTGGAATGTGGAAGGGGGAGGTTGCAGTGAGCCAAGATCGAGCCACTGCACTCCAGCCTGGGCGACAAAAACTGTCTCAAAAACAAACAAACAAACAAACAAAAAACTGACATTTAAAATAGAGACAGGGTCTTGCTTGTTTGTTGCCCAGAAGGCTGGCCTCAAGCAGTCCTCCCTCCTCAGTCTCTGAAATTGCTAGTATTACAGGCATGAGCCACCATGCCTGGCCCACAGTATTATTTTATAAAGTATAAAGATATACGTATTTTTAAAACTTCTTTTAAAATAAAAAGAATATATATACAAATAGATTTTTTCTTTTGAAGACAGGGTGTGGCTGTCGCCTAGGCTGGAGTCCAGTGGTGCAATCATAGCTCACTGCAGCCTCGAACTCCTGGCCTCAAGTGATCCTCCTTCCTCGCCATCCCAAAGCTCTGGGATTACAAGTATGAACCACTTGCACCTGGTCTGATCTAGTTTTTTAAGCATGAGAACTGGGCTGTGCTGTAAATGTGGCTTCTCTGAATTGAGATGGGCTATAGGTAGAAAATACACACTGAATTTCAAAGGTTACGTGAGCAGAAGAATATAAAATATCTCAATTTTTTATATCGATGACAAGTTGAGATGACAATATTTTGGAATATATTGGGTTAAATAAAAATTTGTTTCACCAGTTTCTTTTTATTTTTATTTTATTTTTTTGAGATGGAGTCTCGCTCTTGTTGGCCAGGCTGGAGTACAGTGGCACTATCTCGGCTCACTGTAACCTCCGCCTCCTGGGTTTAAGTGATTCTCCTGCCTCAGCCTCCTGAGTAGCTGGGATTGCAGGCATATACCACCATGCCCGGCTAATTTTTGTATTTTTAGTACAGACGGGGTTTCACCATGTTGGTCAGGCTGGTCTCGGACTCTTGACCTCAGGTGATCCGCCCACCTCAGCCTCCCAAAGTGCTGGGATTACAGGGGTGAGCCACCATGCCCAGCCTATTTTAAAATGTTTAGATGTGTCTATGGAAAATTTTATTTTATTTTATTTTATTTATTTATTTATTTTTGAGACAGAGTCTCGCTCTGTCACCCGGGCTGGAGTGCAGTGGCCTGATCTCAGCTCACTACAAGCTCTGCTTCCCGGGTTCACGCCATTCTCCTGCCTCAGCCTCCCAAGTAGCTGGGACTACATGTGCCCGCCACCACGCCCGGCTAATTTTTTGTTTGTTTGTTTGTATTTTTAGTAGAGACAGGGTTTCACTGTGTTAGCCAGGATAGTCTTGATCTCCTGACCTCGTGATCCACCCGCCTCAGCCTCCCAAAGTGCTGGGATTATAGGCGTGAGCCACCGCACCGGCTGGAAAATTTTTAAATCATCCACGTGTCTCATAGTTTTGCGGGACATCTGTAGACCCCAGGAGAGCTGCCTGCTGATCAGAACTCATTCCCCAGCCTGGCTCAGCTGGATGCCTCACAGTTCCCAAACAGTCCTGTTTTCTTGCCTCCACGCCTTTGCACCAGGGGTCCTTTCCCTGGCGCACTTCCCTCCTGACCTTTCCTCTGGGCTCATCTCCTGCCCAGTGAAGCCTTCCCTGATCCTGCAGTCACATCTGAAGCACCCGGCCCGCTCTGCGTGTGTGGTAACTGGTGCTGCACTGGTCTTTCCCCTCGACTAGATCACTAACCACGCTGACCAACATTTGAATGGAATTTAAATTCCACAAAATATTTTTCACAGCCACCATCTAGTTTTGTTGTTGTTGTTGTTTTGAGATAGGGTCTCCCTCTGTCA        30      .       REPTYPE=SIMPLEINS;BREAKSIMLENGTH=1;REFWIDENED=chr1:23884346-23884346    GT:AD   1|1:0,2
chr1    25405592        .       T       TGCAATGAGCTATGATTGTACCACTGGGAAGTGACAAAGGGCACCCTGGGGGATTTCAAATGGTGGTGGCCCTGGTTTGGTGTTGCTGCCAGGTGAGTCCTTAAGCTATA  30      .       REPTYPE=SIMPLEDEL;BREAKSIMLENGTH=8393;REFWIDENED=chr1:25415381-25405617 GT:AD   1|1:0,2
...

[ACEnglish]

This error occurs whenever pysam (a wrapper around htslib) encounters a monomorphic reference variant call and there is an attempt to access ALT records. You can filter these sites and create a new input for truvari with the commands:

bcftools view -c 1 input.vcf  -O z -o new_file.vcf.gz
tabix new_file.vcf.gz

See 31e4a49