segfault with contig in fasta but not bam

[dmaticzka]

Hey, nice Tool and Paper!

I think I got a segfault because chr6_ssto_hap7 is in my genome fasta but not mapped in the bam. How about skipping these cases? Would be nice if one could use a generic genome fasta, independent of the bam files (I just tested one of the published eCLIP bams).

Parse BAM region 
... observations loaded
F: Parse covered intervals and get observations  ...i1: 0 i2: 48129895
R: Parse covered intervals and get observations  ...i1_R: 0 i2_R: 48129895
 Excluded 0 covered intervals from analysis because of internal polyA sites! 
 Excluded 0 covered intervals from analysis because of internal polyU sites! 
 No. of remaining intervals: 17269   F: 8631   R: 8638
 No. of remaining intervals after cleaning up: 7843
Parse alignments ... 
Open Bam and Bai file ... 
ERROR: Contig chr6_ssto_hap7 not known.
F: Parse covered intervals and get observations  ...i1: 0 i2: 4928567
Command terminated by signal 11

[skrakau]

Hi,

Thanks for pointing this out! Indeed this should not be the case. I will have a look at this in the next days.

Cheers, Sabrina

[dmaticzka]

Cool, thank you!

One small question: pureCLIP does not handle replicates natively, or does it? Any suggestions?

Cheers, Daniel

On Sat, Nov 18, 2017 at 4:23 PM, Sabrina Krakau notifications@github.com wrote:

Hi,

Thanks for pointing this out! Indeed this should not be the case. I will have a look at this in the next days.

Cheers, Sabrina

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Daniel Maticzka Dr. rer. nat. Lehrstuhl für Bioinformatik Institut für Informatik Albert-Ludwigs-Universität Freiburg

Tel: (+49) 761 203 97529 Fax: (+49) 761 203 7462 Mail: maticzkd@informatik.uni-freiburg.de

[skrakau]

Hi Daniel,

PureCLIP doesn't handle replicates yet, so far we used replicates only for evaluation (while correcting for reproducible biases). For the general analysis we simply merged them.

Cheers, Sabrina

[skrakau]

Fixed in version 1.0.3