"Error encountered querying alignments: java.lang.NullPointerException" while reading bam file

[Paul Shannon]

Dear igv team.

We get the error printed in the title, above, when loading a bam file created via these steps - a bam file which has been run through samtools, so should be legitimate.

The processing steps leading to the bam file include:

  - deconvolution from Illumina flo cell (specific to single cell protocol)

  - trimming of polyA

  - mapping of only R2 using snapr

  - sorting the snapr bam file with samtools

Maybe relevant, maybe not, is that expanded cigar strings (the default for snapr) are used int the file.

Our smallish single cell file includes only mapped reads (again using samtools).

We are using igv version 2.3.68.  We'd be glad to provide the 17M file.

Thanks!

 - Paul

[Jim Robinson]

Hi Paul,

Could you open an issue in the igv git repo?   Also,  attach your igv.log file, or contents thereof.    Having the bam would of course be helpful,  if you have somewhere I can pull it from note that in the git comments.

Jim

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