Tags: WordLess-ChuanJun/samtools
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Release 1.6: New markdup command; sort improvements * Added new markdup sub-command and '-m' option for fixmate. Used together, they allow duplicates to be marked and optionally removed. This fixes a number of problems with the old 'rmdup' sub-command, for example samtools issue samtools#497. 'rmdup' is kept for backwards compatibility but 'markdup' should be used in preference. * Sort is now much better at keeping within the requested memory limit. It should also be slightly faster and need fewer temporary files when the file to be sorted does not fit in memory. (samtools#593; thanks to Nathan Weeks.) * Sort no longer rewrites the header when merging from files. It can also now merge from memory, so fewer temporary files need to be written and it is better at sorting in parallel when everything fits in memory. * Both sort and merge now resolve ties when merging based on the position in the input file(s). This makes them fully stable for all ordering options. (Previously position sort was stable, but name and by tag sorts were not). * New --output-qname option for mpileup. * Support for building on Windows using msys2/mingw64 or cygwin has been improved.
Release 1.5 [Solstice Release] (21st June 2017) -------------------- * Samtools fastq now has a -i option to create a fastq file from an index tag, and a -T option (similar to -t) to add user specified aux tags to the fastq header line. * Samtools fastq can now create compressed fastq files, by giving the output filenames an extention of .gq, .bgz, or .bgzf * Samtools sort has a -t TAG option, that allows records to be sorted by the value of the specified aux tag, then by position or name. Merge gets a similar option, allowing files sorted this way to be merged. (samtools#675; thanks to Patrick Marks of 10xgenomics).
Release 1.4.1 (8th May 2017) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~ * Added options to fastq to create fastq files from BC (or other) tags. * Samtools view has gained a -G <flags> option to exclude on all bits set. For example to discard reads where neither end has been mapped use "-G 12". * Samtools cat has a -b <fofn> option to ease concatenation of many files. * Added misc/samtools_tab_completion for bash auto-completion of samtools sub-commands. (samtools#560) * Samtools tview now has J and K keys for verticale movement by 20 lines. (samtools#257) * Various compilation / portability improvements. * Fixed issue with more than 65536 CIGAR operations and SAM/CRAM files. (samtools#667)
Release 1.4 (13 March 2017) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Noteworthy changes in samtools: * Fixed Issue samtools#345 - out-by-one error in insert-size in samtools stats * bam_split now add a @pg header to the bam file * Added mate cigar tag support to fixmate * Multi-threading is now supported for decoding BAM and CRAM (as well as the previously supported encoding). Most commands that read BAM or CRAM have gained an -@ or --threads arguments, providing a significant speed bonus. For commands that both read and write files the threads are shared between decoding and encoding tasks. * Added -a option to samtools mpileup to show all locations, including sites with zero depth; repeating the option as -aa or -a -a additionally shows reference sequences without any reads mapped to them (samtools#496). * The mpileup text output no longer contains empty columns at zero coverage positions. Previously it would output "...0\t\t..." in some circumstances (zero coverage due to being below a minumum base quality); this has been fixed to output as "...0\t*\t*..." with placeholder '*' characters as in other zero coverage circumstances (see PR samtools#537). * To stop it from creating too many temporary files, samtools sort will now not run unless its per-thread memory limit (-m) is set to at least 1 megabyte (samtools#547). * The misc/plot-bamstats script now has a -l / --log-y option to change various graphs to display their Y axis log-scaled. Currently this affects the Insert Size graph (PR samtools#589; thanks to Anton Kratz). * Fixmate will now also add and update MC (mate CIGAR) tags.
Samtools release 1.3.1: bug fixes, notably sort temporary files * The sort command creates any needed temporary files alongside the final output file (similarly to the pre-1.3 behaviour), and now aborts when it detects a collision with another sort invocation's temporary files. When the -T PREFIX option specified is a directory (or when sorting to standard output), a random component is now added to temporary filenames to try to avoid collisions (samtools#432, samtools#523, samtools#529, samtools#535, PR samtools#530). * All samtools commands now check for I/O errors more carefully, especially when writing output files (samtools#111, samtools#253, samtools#470, PR samtools#467). * Build fixes for 32-bit systems; be sure to run configure on such systems to enable large file support and access to 2GiB+ files. * The fasta/fastq/bam2fq command no longer ignores reads when the -s option is used (samtools#532). * The fastq -O option no longer crashes on reads that do not have an OQ tag field (samtools#517). * The merge and sort commands now handle (unusual) BAM files that have no textual @sq headers (samtools#548, samtools#550). * Sorting files containing @co headers no longer duplicates the comment headers, which previously happened on large sorts for which temporary files were needed (samtools#563). * The rmdup and view -l commands no longer crash on @rg headers that do not have a LB field (samtools#538). * Fixed miscellaneous issues samtools#128, samtools#130, samtools#131, samtools#489, and samtools#514.
Samtools release 1.3: many improvements, fixes, new commands * The obsolete "samtools sort in.bam out.prefix" usage has been removed. If you are still using -f, -o, or out.prefix, convert to use -T PREFIX and/or -o FILE instead. (samtools#295, samtools#349, samtools#356, samtools#418, PR samtools#441; see also discussions in samtools#171, samtools#213.) * The "bamshuf" command has been renamed to "collate" (hence the term bamshuf no longer appears in the documentation, though it still works on the command line for compatibility with existing scripts). * The mpileup command now outputs the unseen allele in VCF/BCF as <*> rather than X or <X> as previously, and now has AD, ADF, ADR, INFO/AD, INFO/ADF, INFO/ADR --output-tags annotations that largely supersede the existing DV, DP4, DPR annotations. * The mpileup command now applies BAQ calculations at all base positions, regardless of which -l or -r options are used (previously with -l it was not applied to the first few tens of bases of each chromosome, leading to different mpileup results with -l vs. -r; samtools#79, samtools#125, samtools#286, samtools#407). * Samtools now has a configure script which checks your build environment and facilitates choosing which HTSlib to build against. See INSTALL for details. * Samtools's Makefile now fully supports the standard convention of allowing CC/CPPFLAGS/CFLAGS/LDFLAGS/LIBS to be overridden as needed. Previously it listened to $(LDLIBS) instead; if you were overriding that, you should now override LIBS rather than LDLIBS. * A new addreplacerg command that adds or alters @rg headers and RG:Z record tags has been added. * The rmdup command no longer immediately aborts (previously it always aborted with "bam_get_library() not yet implemented"), but remains not recommended for most use (samtools#159, samtools#252, samtools#291, samtools#393). * Merging files with millions of headers now completes in a reasonable amount of time (samtools#337, samtools#373, samtools#419, samtools#453; thanks to Nathan Weeks, Chris Smowton, Martin Pollard, Rob Davies). * Samtools index's optional index output path argument works again (samtools#199). * Fixed calmd, targetcut, and potential mpileup segfaults when given broken alignments with POS far beyond the end of their reference sequences. * If you have source code using bam_md.c's bam_fillmd1_core(), bam_cap_mapQ(), or bam_prob_realn_core() functions, note that these now take an additional ref_len parameter. (The versions named without "_core" are unchanged.) * The tview command's colour scheme has been altered to be more suitable for users with colour blindness (samtools#457). * Samtools depad command now handles CIGAR N operators and accepts CRAM files (samtools#201, samtools#404). * Samtools stats now outputs separate "N" and "other" columns in the ACGT content per cycle section (samtools#376). * Added -a option to samtools depth to show all locations, including zero depth sites (samtools#374). * New samtools dict command, which creates a sequence dictionary (as used by Picard) from a FASTA reference file. * Samtools stats --target-regions option works again. * Added legacy API sam.h functions sam_index_load() and samfetch() providing bam_fetch()-style iteration over either BAM or CRAM files. (In general we recommend recoding against the htslib API directly, but this addition may help existing libbam-using programs to be CRAM-enabled easily.) * Fixed legacy API's samopen() to write headers only with "wh" when writing SAM files. Plain "w" suppresses headers for SAM file output, but this was broken in 1.2. * "samtools fixmate - -" works in pipelines again; with 1.0 to 1.2, this failed with "[bam_mating] cannot determine output format". * Restored previous "samtools calmd -u" behaviour of writing compression level 0 BAM files. Samtools 1.0 to 1.2 incorrectly wrote raw non-BGZF BAM files, which cannot be read by most other tools. (Samtools commands other than calmd were unaffected by this bug.) * Restored bam_nt16_nt4_table[] to legacy API header bam.h. * Fixed bugs samtools#269, samtools#305, samtools#320, samtools#328, samtools#346, samtools#353, samtools#365, samtools#392, samtools#410, samtools#445, samtools#462, samtools#475, and samtools#495.
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