I am trying to re-count a bunch of bam files that I have previously opened without problems in easyRNAseq and GenomicAlignments. But now I get. The bam files are seemingly valid and can be accessed by samtools, but the header contains few duplicated entries.
reads = readGAlignments('test.fastq.gz.clipped_M.bam.sorted.bam'
Error in GAlignments(seqnames = bamcols$rname, pos = bamcols$pos, cigar = bamcols$cigar, : 'seqlengths' must be an integer vector with unique names In addition: Warning message: In `levels<-`(`*tmp*`, value = if (nl == nL) as.character(labels) else paste0(labels, : duplicated levels in factors are deprecated
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