problem in displaying individual paired-end reads on gbrowse instance

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problem in displaying individual paired-end reads on gbrowse instance

Vipin TS
Hello Gbrowse team,

Recently I noticed that, on our public Gbrowse instance (http://gbrowse.cbio.mskcc.org/), the individual read display is not properly rendering. (works fine for single-end reads)

The error message from apache log:

RenderPanels error: Can't locate object method "tid" via package "Bio::DB::Bam::SplitAlignmentPart" at /data/gb/perl5/lib/perl5/x86_64-linux-thread-multi//Bio/DB/Sam.pm line 1991.
[Wed Oct 01 11:08:28 2014] [warn] [client 172.21.50.98] mod_fcgid: stderr: [19371] rendering error track: Can't locate object method "tid" via package "Bio::DB::Bam::SplitAlignmentPart" at /data/gb/perl5/lib/perl5/x86_64-linux-thread-multi//Bio/DB/Sam.pm line 1991. at /data/gb/gbrowse/lib/perl5/x86_64-linux-thread-multi//Bio/Graphics/Browser2/Render.pm line 3678., referer: http://gbrowse.cbio.mskcc.org/gb/gbrowse/human/

Here in my track configurations:
[TSkim:database]
db_adaptor    = Bio::DB::Sam
db_args       = -bam    /data/gb/gbrowse/www/data/TSkim_uniq.bam
                -split_splices 1

[TSkim_reads:1001]
feature      = coverage
database     = TSkim
glyph        = wiggle_xyplot
bgcolor      = red
height       = 40
fgcolor      = black
min_score    = 0
scale        = three
label          = 0
category     = 4. RNA-Sequencing (ARTS2 project)
key          = SRR534327

[TSkim_reads]
feature      = read_pair
database         = TSkim
parts_overlap= 1
glyph            = segments
draw_target    = 1
show_mismatch  = 1
mismatch_color = red
indel_color    = green
height         = 3
label   = 0
label density = 50
fgcolor      = black
bgcolor      = green
maxdepth     = 2
box_subparts = 2
stranded     = 1
connector = dashed
bump           = fast
category     = 4. RNA-Sequencing (ARTS2 project)
key          = SRR534327

The above configuration works fine for displaying the coverage tracks, but when it comes to individual read display the error happens.

I am using Bio::DB::Sam version 1.38, from the http://search.cpan.org/~lds/Bio-SamTools-1.38/ distribution package page, I am seeing the "Bio::DB::Bam::SplitAlignmentPart " seems like a deprecated module.

Can anyone please let me know is there any issue with the track configuration? or a better way for displaying paired end reads.

Thank you,

Vipin | Rätsch Lab

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