htslib release 1.14: Features and Updates -------------------- * Added a keep option to bgzip to leave the original file untouched. This brings bgzip into line with gzip. (PR #1331, thanks to Alex Petty) * "endpos" has been added to the filter language, giving the position of the rightmost mapped base as measured by the CIGAR string. For unmapped reads it is the same as "pos". (PR #1307, thanks to John Marshall) * Interfaces have been added to interpret the new base modification tags added to the SAMtags document in samtools/hts-specs#418. (PR #1132) * New API functions hts_flush()/sam_flush()/bcf_flush() for flushing output htsFile/samFile/vcfFile streams. (PR #1326, thanks to John Marshall) * The synced_bcf_reader now sorts lines with symbolic alleles by END tag as well as POS. (PR #1321) * Added synced_bcf_reader options BCF_SR_REGIONS_OVERLAP and BCF_SR_TARGETS_OVERLAP for better control of records that start outside the desired region but overlap it are handled. Fixes samtools/bcftools#1420 and samtools/bcftools#1421 raised by John Marshall. (PR #1327) * HTSlib will now accept long-cigar CG:B: tags made by htsjdk which don't quite follow the specification properly (using signed values instead of unsigned). Thanks to Colin Diesh for reporting an example file. (PR #1317) * The warning printed when the BGZF reader finds a file with no EOF block has been changed to be less alarming. Unfortunately some third-party BGZF encoders don't write EOF blocks at the end of files. Thanks to Keiran Raine for reporting an example file. (PR #1323) * The FASTA and FASTQ readers get an option to skip over the first item on the header line, and use the second as the read name. It allows the original name to be restored on some of the fastq files served from the European Nucleotide Archive (ENA). (PR #1325) * HTSlib is now more strict when parsing the VCF samples line (beginning #CHROM). It will only accept tabs between the mandatory field names and sample names must be separated with tabs. (PR #1328) * HTSlib will now warn if it looks like the header has been corrupted by diagnostic messages from the program that made it. This can happen when using `nohup`, which by default mixes stdout and stderr into the same stream. (PR#1339, thanks to John Marshall) * File format detection will now recognise signatures for XZ, Zstd and D4 files (note that HTSlib will not read them yet). (PR #1340, thanks to John Marshall) Build changes ------------- These are compiler, configuration and makefile based changes. * Some redundant tests have been removed from the test harness, speeding it up. (PR #1308) * The version.sh script now works better on shallow checkouts. (PR #1324) * A check-untracked Makefile target has been added to catch untracked files (mostly) left by the test harness. (PR #1324) Bug fixes --------- * Fixed a case where flushing the thread pool could very occasionally cause a deadlock. (PR #1309) * Fixed a bug where some CRAM files could fail to decode if the required_fields option was in use. Thanks to Matt Sexton for reporting the issue. (PR #1314, fixes samtools/samtools#1475) * Fixed a regression where the S3 plugin could not read public files unless you supplied some Amazon credentials. Thanks to Chris Saunders for reporting. (PR #1332, fixes samtools/samtools#1491) * Fixed a possible CRAM thread deadlock discovered by @ryancaicse. (PR #1330, fixes #1329) * Some set-but-unused variables have been removed. (PR #1334) * Fixed a bug which prevented "flag.read2" from working in the filter language unless it was at the end of the expression. Thanks to Vamsi Kodali for reporting the issue. (PR #1342) * Fixed a memory leak that could happen if CRAM fails to inflate a LZMA block. (PR #1340, thanks to John Marshall)