Bug #66138 for Bio-SamTools: _coverage function should not count reads that skip the input region

Hi Bio-Samtools Team, I have noticed a problem of getting coverage of RNA-Seq reads. These reads usually have long skips in middle (i.e. long "N" in CIGAR string) to cross introns. However, if I use the _coverage function on an intron, I still get very high coverage because the function counts the reads that cross the introns to map to exons at both ends . The solution, as you already mentioned in the function, is to use pileup instead in the _coverage function. The latest samtools pileup function returns bam_pileup1_t data structure with is_refskip and is_del flags to be used to ignore reads that skip the region. I am using Bio-Samtools 1.27 by Perl 5.8.9 on Linux64. Thanks, Yi-Shiou Chen Accelrys If you do not wish to register with Bitcard, please report your bug by sending email to: bug-Bio-SamTools [at] rt.cpan.org. Try to include any information you think might help the developer isolate, reproduce and fix your problem. Be sure to include at least the following information: * Distribution name and version (For example, "DBIx-SearchBuilder-0.46") * Perl version (Find this by running the command perl -v) * Operating System vendor and version (Find this by running the command uname -a) Other things that are often helpful: * Details about your operating environment that might be related to the issue being described * Exact cut and pasted error or warning messages * The shortest, clearest code you can manage to write which reproduces the bug described. * A patch against the latest released version of this distribution which fixes this bug. [cid:image001.gif@01CBD422.D952A600] [cid:image002.gif@01CBD422.D952A600] Yi-Shiou Chen Principal Engineer Accelrys, Inc. 10188 Telesis Court, Suite 100 San Diego, CA 92121, USA +858 799 5610 [cid:image003.gif@01CBD422.D952A600]<http://twitter.com/Accelrys> [cid:image004.gif@01CBD422.D952A600] <http://www.linkedin.com/companies/6434/Accelrys?trk=pro_other_cmpy> [cid:image005.gif@01CBD422.D952A600] <http://blog.accelrys.com/> Stay Connected with Accelrys and the Scientific & Engineering Community Blog<http://blog.accelrys.com/> | Forum<http://accelrys.org/> | Website<http://accelrys.com/> | Support<http://accelrys.com/services/support.html>