Created attachment 385414 [details, diff] include bam headers With the upgrade to samtools=1.0, the package no longer includes the bam headers in /usr/include/bam/*. I added a patch to install the headers with the package, as they are required to build e.g. cufflinks-1.3.1 or tophat-2.0.9::science. cufflinks builds with problems including this patch, tophat still requires compatibility patches for the new versions from upstream [announced to be fixed within 2 weeks, https://groups.google.com/forum/#!topic/tuxedo-tools-users/BVNDDmInU0A]. This also partially solves incompatibility between dev-perl/Bio-SamTools and samtools-1.0 as brought up in https://bugs.gentoo.org/show_bug.cgi?id=523568. However, there may be further issues when packages look for htslib headers in /usr/include/bam instead of /usr/include/htslib, as is the case in #523568. You may want to consider to put htslib headers in include/bam/* to avoid similar issues, but I'm not entirely sure what is the best approach here.
+*samtools-1.0-r1 (25 Sep 2014) + + 25 Sep 2014; Justin Lecher <jlec@gentoo.org> +samtools-1.0-r1.ebuild, + +files/samtools-1.0-buildsystem.patch: + Install bam headers and create libbam.so, #523644 +
