Tags: andy-thomason/htslib
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HTSlib patch release 1.3.2: bin bug fix, RTLD_GLOBAL plugins * Corrected bin calculation when converting directly from CRAM to BAM. Previously a small fraction of converted reads would fail Picard's validation with "bin field of BAM record does not equal value computed" (SAMtools issue samtools#574). * Plugins can now signal to HTSlib which of RTLD_LOCAL and RTLD_GLOBAL they wish to be opened with -- previously they were always RTLD_LOCAL.
HTSlib release 1.3.1: bug fix release, notably error checking * Improved error checking and reporting, especially of I/O errors when writing output files (samtools#17, samtools#315, PR samtools#271, PR samtools#317). * Build fixes for 32-bit systems; be sure to run configure to enable large file support and access to 2GiB+ files. * Numerous VCF parsing fixes (samtools#321, samtools#322, samtools#323, samtools#324, samtools#325; PR samtools#370). Particular thanks to Kostya Kortchinsky of the Google Security Team for testing and numerous input parsing bug reports. * HTSlib now prints an informational message when initially creating a CRAM reference cache in the default location under your $HOME directory. (No message is printed if you are using $REF_CACHE to specify a location.) * Avoided rare race condition when caching downloaded CRAM reference sequence files, by using distinctive names for temporary files (in addition to O_EXCL, which has always been used). Occasional corruption would previously occur when multiple tools were simultaneously caching the same reference sequences on an NFS filesystem that did not support O_EXCL (PR samtools#320). * Prevented race condition in file access plugin loading (PR samtools#341). * Fixed mpileup memory leak, so no more "[bam_plp_destroy] memory leak [...] Continue anyway" warning messages (samtools#299). * Various minor CRAM fixes. * Fixed documentation problems samtools#348 and samtools#358.
HTSlib release 1.3, plugins, libcurl, CRAM v3.0, bug fixes * Files can now be accessed via HTTPS and Amazon S3 in addition to HTTP and FTP, when HTSlib is configured to use libcurl for network file access rather than the included basic knetfile networking. * HTSlib can be built to use remote access hFILE backends (such as iRODS and libcurl) via a plugin mechanism. This allows other backends to be easily added and facilitates building tools that use HTSlib, as they don't need to be linked with the backends' various required libraries. * fai_build() and samtools faidx now accept initial whitespace in ">" headers (e.g., "> chr1 description" is taken to refer to "chr1"). * tabix --only-header works again (was broken in 1.2.x; samtools#249). * HTSlib's configure script and Makefile now fully support the standard convention of allowing CC/CPPFLAGS/CFLAGS/LDFLAGS/LIBS to be overridden as needed. Previously the Makefile listened to $(LDLIBS) instead; if you were overriding that, you should now override LIBS rather than LDLIBS. * Fixed bugs samtools#168, samtools#172, samtools#176, samtools#197, samtools#206, samtools#225, samtools#245, samtools#265, samtools#295, and samtools#296.
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