plot-bamstats fails for new versions of samtools/develop

[nc6]

bamstats files generated using the latest samtools/develop are failing to plot correctly using the corresponding version of plot-bamstats:

Tested on version b44c5e4, plot-bamstats fails with the following error:

"carl-develop/quals-hm.gp", line 142: Scan size of matrix is zero

The command exited with non-zero status 256:
    gnuplot carl-develop/quals-hm.gp

 at /nfs/users/nfs_n/nc6/work/samtools/misc/plot-bamstats line 31.
    main::error("The command exited with non-zero status 256:\x{a}\x{9}gnuplot carl-de"...) called at /nfs/users/nfs_n/nc6/work/samtools/misc/plot-bamstats line 283
    main::plot("carl-develop/quals-hm.gp") called at /nfs/users/nfs_n/nc6/work/samtools/misc/plot-bamstats line 779
    main::plot_qualities(HASH(0x161ace0)) called at /nfs/users/nfs_n/nc6/work/samtools/misc/plot-bamstats line 14

[pd3]

Thank you for noticing, fixed now.

[nc6]

Thanks for the speedy fix!

[ozagordi]

I'm having the same problem with version 0.2.0-rc11

[user@host samtools]$ ./misc/plot-bamstats -p plot/ file.bam.bc
Could not find/open font when opening font "arial", using internal non-scalable font
Could not find/open font when opening font "arial", using internal non-scalable font
Could not find/open font when opening font "arial", using internal non-scalable font
Could not find/open font when opening font "arial", using internal non-scalable font
"plot/quals-hm.gp", line 202: Scan size of matrix is zero

The command exited with non-zero status 256:
        gnuplot plot/quals-hm.gp

 at ./misc/plot-bamstats line 31
    main::error('The command exited with non-zero status 256:\x{a}\x{9}gnuplot plot/qu...') called at ./misc/plot-bamstats line 283
    main::plot('plot/quals-hm.gp') called at ./misc/plot-bamstats line 778
    main::plot_qualities('HASH(0xbeb418)') called at ./misc/plot-bamstats line 14
[user@host samtools]$ samtools --version
samtools 0.2.0-rc11
Using htslib 0.2.0-rc11
Copyright (C) 2014 Genome Research Ltd.

[pd3]

Could you please check with the latest develop version? This page describes how get the code from git http://samtools.github.io/bcftools/
Cheers,

[ozagordi]

I was already on develop, but for the sake of security I cloned again,
recompiled and reran. Same error. I understand that the insert sizes are
missing (I have single end reads) as in the bam.bc file I read

# Insert sizes. Use `grep ^IS | cut -f 2-` to extract this part. The columns are: pairs total, inward oriented pairs, outward oriented pairs, other pairs
# Read lengths. Use `grep ^RL | cut -f 2-` to extract this part. The columns are: read length, count
RL      75      17817

[pd3]

OK, good. Would you mind sharing your output file so that I can learn more about the bam?

[ozagordi]

I can certainly share the stat file. The full bam would be complicated (patient sample).

[pd3]

I am not interested in the bam itself, only the output from samtools stats, sorry if there was any confusion about this. I just want to make sure that I fix also any other issues caused by this type of bam.

[ozagordi]

Just sent to you.
Thanks.

[pd3]

Thank you for the testing data, it's fixed now by 88f7ca9. For now the code is on a separate 'stats' branch which you can get by git pull && git checkout stats or git clone --branch=stats git://github.com/samtools/samtools.git

[ozagordi]

It now produces the graphs, thanks for solving it.