samtools tview special character
I am trying to examine some loci in an aligned rnaseq bam and having trouble interpreting certain lines.
$ samtools tview -p 19:18758255 -d T M_2/STAR/M_2.Aligned.sortedByCoord.out.bam --reference /resources/genomes/GRCh37/fasta/b37.fasta
18758261 18758271 18758281 18758291 18758301 18758311 18758321
CCTTTTTCTGATATTTGTGTGTGTGTGTGTGTCTTACCCTTTGGTTTTAGGGAATGTTTTAGATTTGGTGTTAAGAGGCC
KK.....K..K.K...................K..KKKK.........K...KK......K.K.........KK.K....
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<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
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..
I have no idea what the arrows mean. my guess is a spanning fragment, since it might be more common in rnaseq, and the direction of the arrow tells you the orientation of the read? some tview cases like this have lines at the end with actually sequences in them which stuff like t,,,,,,,,,,,,,,,, which i'm more familiar with.
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Pierre Lindenbaum
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from the mountains
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reference skip (cigar=N): https://github.com/samtools/samtools/blob/develop/bam_tview.c#L252
} else c = p->is_refskip? (bam_is_rev(p->b)? '<' : '>') : '*';
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