Unrecognized nucleotide 'B' error when sequence field in BAM file omitted #64
Description
Describe the bug
When using Rsamtools::pileup and the bam file provided contains records where the sequence field is omitted (as *), this error message is shown:
Error in value[[3L]](cond) : Unrecognized nucleotide 'B'
To Reproduce
Please provide minimal R code to reproduce the example.
A bam file with a record without sequence:
@HD VN:1.6 SO:coordinate
@SQ SN:chr1 LN:248956422
read1 0 chr1 100 60 5M * 0 0 ACTGT FFFFF NM:i:0 AS:i:5
read1 256 chr1 5000 30 5M * 0 0 * * NM:i:0 AS:i:4
and
Rsamtools::pileup('example.bam')
Expected behavior
Suggesting the user this is due to sequence field unavailable, or skipping the record.
sessionInfo
> sessionInfo()
R version 4.4.2 (2024-10-31)
Platform: x86_64-pc-linux-gnu
Running under: Arch Linux
Matrix products: default
BLAS: /usr/lib/libblas.so.3.12.0
LAPACK: /usr/lib/liblapack.so.3.12.0
locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
[3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8
[5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8
[7] LC_PAPER=en_US.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
time zone: Australia/Melbourne
tzcode source: system (glibc)
attached base packages:
[1] stats4 stats graphics grDevices utils datasets methods
[8] base
other attached packages:
[1] Rsamtools_2.20.0 Biostrings_2.72.1 XVector_0.44.0
[4] GenomicRanges_1.56.1 GenomeInfoDb_1.40.1 IRanges_2.38.1
[7] S4Vectors_0.42.1 BiocGenerics_0.50.0
loaded via a namespace (and not attached):
[1] R6_2.5.1 codetools_0.2-20 zlibbioc_1.50.0
[4] GenomeInfoDbData_1.2.12 parallel_4.4.2 UCSC.utils_1.0.0
[7] bitops_1.0-8 compiler_4.4.2 httr_1.4.7
[10] tools_4.4.2 jsonlite_1.8.8 crayon_1.5.3
[13] BiocParallel_1.38.0