Hi,
I've been trying to use the Trackster visualisation with a BAM file, and find it segfaults quite regularly, with the (somewhat unhelpful) message
./run.sh: line 47: 13782 Segmentation fault (core dumped) python ./scripts/paster.py serve universe_wsgi.ini $@
Using gdb I have gotten the following info:
Program received signal SIGSEGV, Segmentation fault. [Switching to Thread 0x4a6b5940 (LWP 13800)] 0x00002adeee8c7937 in get_chunk_coordinates (idx=0xffffffffb0018da0, tid=0, beg=0, end=-1341883296, cnt_off=0x2aaab0016600) at samtools/bam_index.c:501 501 samtools/bam_index.c: No such file or directory. in samtools/bam_index.c
However the BAM index should be getting created and stored as part of the meta data.
I also notice the pysam library being used is 0.1.1, whereas they are up to 0.3.1.
Any help greatly appreciated, the visualisation looks very good when it's working.
I am able to send the BAM file I'm using if necessary.
Cheers, --Alan