[med-svn] samtools branch master updated (5761c3f -> 28391e5)
Charles Plessy
plessy at moszumanska.debian.org
Fri Nov 22 05:53:52 UTC 2013
This is an automated email from the git hooks/post-receive script.
plessy pushed a change to branch master
in repository samtools.
omits 5761c3f samtools (0.1.19-1) unstable; urgency=low
omits ddcd54e Use NEWS as upstream changelog.
omits e13bb5e Normalised VCS URLs.
omits dce5436 URL to the latest upstream changelog.
omits 1e6d442 New tools ace2sam, bamcheck, plot-bamcheck, r2plot.lua and vcfutils.lua.
omits 5e92ced Moved to GitHub.
omits fc32243 Harden by concatenating Debian's LDFLAGS and CPPFLAGS in CFLAGS.
omits 8d8550e Pass -lpthread when compiling calDepth.
omits 3e7e0ec Rename no-pileup-tests.patch fix_example_makefile.patch.
omits 9c0e543 Refreshed patches.
omits e194f9e Removed fix_float_tag.patch, corrected upstream.
omits 81ad760 Conforms to Policy version 3.9.4.
omits a1b1b00 Deleted DM-Upload-Allowed field.
omits 6f75b48 Normalised with cme (from the libconfig-model-perl package).
omits 2f2d5c5 Collapsed copyright notices from main holders.
omits f851d49 Binary files (re-)introduced by the update.
omits a0d2c5c New upstream release, no new license nor copyright statements.
omits f70aa9a Merge tag 'upstream/0.1.19'
omits cb9bd50 Imported Upstream version 0.1.19
omits 3a22e5b Include 7 digits of the commit id in the changelog entry.
omits cd5dbce added 3 bug fixes
omits 8220f2b Normalised with config-model.
omits 3366988 Bash completion, see https://github.com/arq5x/bash_completion.
omits 3a7e30b Build-depend on Debhelper 9 (see e6882df5b3e4a66100acf69c8f0f213208d16c92).
omits 92876b6 debian/upstream: replace a perfectly valid BibTeX entry which happens to cause problems in the replacement algorith for the tasks pages written by Michael Banck
omits e6882df Pass build flaggs set by dpkg-buildflags via Debhelper.
omits 2dbfbdd Moved DOI and PubMed to the Reference namespace.
omits 5deeed4 Renamed debian/upstream-metadata.yaml to debian/upstream.
omits a0a6520 Do not compress the example binary alignment file.
omits 2d64e9d Mention ‘SAMtools’ in libbam-dev's description, to make it easier to find with apt-cache.
omits 58ef643 Starting the work on next package update.
omits 8ac6060 Uploading 0.1.18-1 to unstable.
omits 9a36c99 Added a DEP 3 header to debian/patches/no-pileup-tests.patch.
omits aa08abe Compress binary packages with xz.
omits d59366b New upstream release.
omits b990d9d Merge commit 'upstream/0.1.18'
omits 0f906da Imported Upstream version 0.1.18
omits 5075acd Uploading samtools_0.1.17-1_amd64.changes.
omits 2347ad6 Patched the example makefile to not use samtools pileup, deprecated.
omits e582623 bcftools.1 and samtools.1 were merged in upstream release 0.1.17.
omits d4f09f4 New upstream release (no new copyright holder nor license statement).
omits e2bd290 Merge commit 'upstream/0.1.17'
omits b301e95 Imported Upstream version 0.1.17
omits 9f4beba Uploaded samtools_0.1.16-1_amd64.changes.
omits 625c4a7 Move the headers to /usr/include/samtools.
omits 20f9616 Distribute transiently sam.h in /usr/include.
omits 4d48f74 Added a configuration file to make it obvious git-buildpackage is used.
omits 4bd59ad New upstream release, introducing two files with new copyright statements.
omits b7c06ea Merge commit 'upstream/0.1.16'
omits 8a8212c Imported Upstream version 0.1.16
omits cdbe062 Uploaded 0.1.15-1 to Sid.
omits 20afc7c New upstream release (no new copyright notices).
omits e42445c Imported Upstream version 0.1.15
omits 0242bdf Merge commit 'upstream/0.1.15'
omits ced7709 # Uploaded samtools version 0.1.14-1.
omits 12a7719 # New upstream release (new copyright notices and licenses proofchecked).
omits fa217aa Imported Upstream version 0.1.14
omits 6828a9a Merge commit 'upstream/0.1.14'
omits 9303e89 # Uploaded 0.1.13 to Sid.
omits 188a91b # bcftools/bcf-fix.pl removed upstream.
omits 4b41b42 # Copyright review of the diff between 0.1.12 and 0.1.13.
omits c346248 Imported Upstream version 0.1.13
omits 1539c89 Merge commit 'upstream/0.1.13'
omits a8ea86b # Install the manual page of bcftools.
omits 7c5e2e2 # Uploaded 0.1.12a-1 to Debian.
omits 39c2403 # Use bzip2 compression for the binary packages and raised DH compat level.
omits cdd6f3c # New usptream release; no change for licenses or copyrights.
omits cd828d5 Merge commit 'upstream/0.1.12a'
omits f2f3968 Imported Upstream version 0.1.12a
omits 78c7059 Merge commit 'upstream/0.1.11'
omits 6a0c6f0 Imported Upstream version 0.1.11
omits e5065a5 # New upstream release.
omits 016b50a Merge commit 'upstream/0.1.10'
omits e3b3a01 Imported Upstream version 0.1.10
omits 349ae4d # New upstream release, and new program: bcftools.
omits 85bb950 # Install bcftools, its manpage, bcf-fix.pl, vcfutils.pl, and new examples.
omits a1eac05 # Incremented Standards-Version to reflect conformance with Policy 3.9.1.
omits 2adb485 # Updated and reformatted debian/copyright according to latest DEP-5 draft.
omits 8e6e7ef # New files in the new upstream release.
omits 8d2494d Imported Upstream version 0.1.9
omits 62781a2 Merge commit 'upstream/0.1.9'
omits cefa180 Added notes on how the package is tested.
omits 4dd37bb New upstream release, with among many changes a new python script.
omits 0497052 Copied from SVN revision 4710 and adapted to Git.
omits d03185b This source package is managed with Git since upstream version 1.7~dfsg.
omits 9ff80e8 Copyright notice bureaucracy.
omits bae891c The 1.8 tarball does not contain Windows binaries anymore.
omits 67801bf Merge commit 'upstream/0.1.8'
omits cb12a86 Imported Upstream version 0.1.8
omits a8151f9 In version 1.8, there are no binary files to remove from the upstream tarball.
omits 81c994d Uploaded package after misc. improvements.
omits 0a8c2ac Tidied the minimalistic razip.1 manual page.
omits 0948127 Simple manpage created with help2man.
omits b492d77 Minor upstream update correcting a build failure.
omits 8af6e7e Merge commit 'upstream/0.1.7a.dfsg'
omits 3a3b721 Imported Upstream version 0.1.7a~dfsg
omits 7899553 Converted to the source format ‘3.0 (quilt)’.
omits cfcfcb6 Update in preparation for new upstream release.
omits 317f5e8 Imported Upstream version 0.1.7~dfsg
omits 63f0c51 Merge commit 'upstream/0.1.7.dfsg'
omits 86a7eb3 Imported Debian patch 0.1.6~dfsg-1
omits 4a17fa7 Imported Upstream version 0.1.6~dfsg
omits d363084 Merge branch 'upstream'
omits 4836a5b Imported Debian patch 0.1.5c-2
omits b78a63d Imported Debian patch 0.1.5c-1
omits b27e003 Imported Upstream version 0.1.5c
adds f93dae0 Create trunk copy
adds d97f59c Fix problem with compiling without curses.
adds 635998c * Merge from branches/dev/ * all future development will happen here at trunk/
adds 38c2703 * merge from branches/dev/ * all future development will happen here
adds fb6c8f2 * samtools-0.1.1-19 * fixed a bug in "merge" command line
adds 6d1982a update documentation and ChangeLog
adds 3c2e62d add a script to convert novo alignment to SAM
adds 307c7ac convert ZOOM to SAM
adds 65baf77 Script for filtering indel results
adds 6c4f7da Release SAMtools-0.1.2
adds a2ef036 * samtools-0.1.2-1 * added flagstat command
adds c738799 * samtools-0.1.2-3 * fixed a bug in generating GLFv2 for indels * improve flagstat report a little bit
adds 69b7f0f Pass LIBS to recursive targets to facilitate building at Broad.
adds 47c65ef fixed a potential memory problem in indexing
adds 136d269 fixed a bug in generating tag AM
adds 4d0009d * output max mapping quality in indel line
adds 091c8d2 * samtools-0.1.2-6 * improve indel caller by setting maximum window size
adds 02884d7 * samtools-0.1.2-7 * fixed a minor bug in flagstat
adds 1355b18 * samtools-0.1.2-7 * fixed a bug in fixmate: SE reads are flagged as BAM_FMUNMAP
adds 8d5d72a * move indel_filter.pl to samtools.pl
adds 3b08b1d Fix annoying segv when invalid region specified.
adds cbb6d03 * samtools-0.1.2-9 * fixed a bug in bam_fetch, caused by completely contained adjacent chunks
adds 7a38b29 * wgsim-0.2.0 * considerable code clean up * print number of substitutions/indels/errors on each read * potentially support SOLiD simulation, though not tested at the moment * wgsim_eval.pl-0.1.2 * change in accordant with wgsim
adds 115b2e9 * wgsim: added a note
adds b24678a * wgsim-0.2.1 * fixed a bug about color read coordinates * fixed a bug in read names * wgsim_eval.pl-0.1.3 * make the script work with color reads
adds bf2e331 * wgsim-0.2.2 * allow to print mismatch information as fastq comment. MAQ does not like long read names.
adds e2bd6d5 * wgsim-0.2.3 * fixed a bug in simulating indels
adds ecbde30 * samtools-0.1.2-10 * fixed a bug in import: core.bin is undefined for unmapped reads * this bug can be alleviated (not completely solved) in bam_index.c * update to GLFv3: pos is changed to offset for better compression
adds 3fe3402 * samtools-0.1.2-11 * use "GLF\3" as the magic for GLFv3 files
adds e981067 * samtools-0.1.2-12 * optionally print SAM header
adds dbdb7c6 * samtools-0.1.2-13 * fixed a minor bug in displaying pileup
adds 1fff321 * samtools-0.1.2-14 * implemented GLFv3
adds 35f8bc0 * samtools-0.1.2-15 * generate RMS of mapQ instead of max mapQ
adds 74ec830 added bam_stat.o to Makefile.lite
adds cb770f1 * soap2sam.pl-0.1.2 * more robust to truncated soap output
adds 42e7568 * samtools-0.1.2-16 * made pileup take a list of proposed indels. An insertion is N at the moment. * added my kstring library for a bit complex parsing of the position list.
adds 98d7949 * samtools-0.1.2-17 * incorporating Nils' changes * rename Makefile to Makefile.std and prepare to add the GNU building systerms (also by Nils)
adds 54ce06b rename Makefile.std as Makefile. GNU building systerm is not ready and may take some time...
adds c311a7f * samtools-0.1.2-18 * fixed a minor bug reported by Nils Homer
adds 0a7b85c * samtools-0.1.2-19 * print the header if requested
adds 5af1150 * samtools-0.1.2-20 * check if file is truncated in flagstat
adds 7c8e419 make the script robust to the bugs in SOAP-2.1.7
adds c8044e2 * samtools-0.1.2-21 * fixed a nasty bug in `fixmate'
adds 461e009 * fixed the problem in the example alignment due to the bug in fixmate
adds 17d530d * samtools-0.1.2-22 * the field separater is TAB only, now
adds 3c65ee9 * samtools-0.1.2-23 * recognize '*' at the QUAL field
adds 8cc87ac * samtools-0.1.2-24 * in merge, gives a warning rather than error if the target sequence length is different * allow empty header
adds 2eeb30e update ChangeLog from "svn log"
adds 65467e1 * samtools-0.1.2-25 * change the pileup indel line to shows the number of alignments actually containing indels
adds ececa9f * samtools.pl-0.1.1 * improve indelFilter to avoid filtering true indels. The new filter relies on the new pileup indel line implemented in samtools-0.1.2-25
adds bea524c proposed NEWS for the new release (have not yet)
adds 5fb8040 * samtools-0.1.2-26 * fixed a bug in rmdup when there are unmapped reads
adds 6d35460 * samtools-0.1.2-27 * fixed a small memory leak in tview
adds 4c63c56 convert NCBI-BLASTN to SAM
adds e2a3ec4 prepare for release 0.1.3
adds 5fa181a * samtools-0.1.2-28 * make samtools more robust to weird input such as empty file
adds 646ba48 Release samtools-0.1.3
adds 713d436 a missing file in Makefile.lite
adds f3f36d0 * samtools-0.1.3-1 * fixed a bug in pileup: the first read in a chromosome may not be printed
adds 7bd63d5 * samtools-0.1.3-2 (r239) * fixed bugs in bam_aux.c (these functions nevered used by samtools) * removed bam_aux_init()/bam_aux_destroy() * added tagview for testing bam_aux
adds 63e4e54 * samtools-0.1.3-3 (r240) * generate MD tag * generate "=" bases * the plain pileup now support "=" bases, but consensus calling and glfgen may fail
adds 0a5f488 * samtools-0.1.3-4 (r242) * fixed a memory leak
adds 6762f53 * samtools-0.1.3-5 (r243) * fixed a long existing bug which may cause memory leak * check MD * consensus calling now works with "=", but indel calling not
adds 99a3d0d * samtools-0.1.3-6 (r244) * fixed segfault for unmapped reads
adds 4158618 * samtools-0.1.3-7 (r246) * incorporated revisions from Nils Homer * enhanced support of displaying color-space reads
adds 5fb51bd fixed various issues about the GNU building scripts
adds e5f885b update INSTALL
adds b524c9a improve large file support in compilation
adds e8865fa added missing files
adds e05bad2 * samtools-0.1.3-8 (r251) * fixed a bug when there are reads without coordinates
adds bd52495 * samtools-0.1.3-9 (r256) * fixed a bug in bam_lpileup.c * I do not know if this also fixes the bug causing assertion failure in the tview
adds 6bbac7b * samtools-0.1.3-10 (r257) * allow hex with "pileup -m"
adds f122286 * samtools-0.1.3-11 (r258) * unify the interface to BAM and SAM I/O
adds 7a36e40 * samtools-0.1.3-12 (r259) * use the new I/O interface in pileup
adds 3341285 update Makefile.am
adds d69cb33 * samtools-0.1.3-13 (r260) * report error for file I/O error
adds 39cfa14 * samtools-0.1.3-14 (r262) * make samopen() recognize @SQ header lines
adds 5453d1b * samtools-0.1.3-15 (r266) * report an error if a non-* reference is present while @SQ is absent
adds 964138e * samtools-0.1.3-16 (r267) * in sam_view.c, changed g_flag_on based on the suggestion by Angie Hinrichs
adds 2f8de7d * samtools-0.1.3-17 (r271) * added 'rmdupse' command
adds 42c0abe change a parameter. It does nothing
adds f6a84f5 * samtools-0.1.3-18 (r273) * rmdupse: do not remove unmapped reads
adds 53fb97c * samtools-0.1.3-19 (r275) * a minor change to the bam1_t struct: added back "void *hash" for the backward compatibility with Bio::DB::Sam
adds 00e3808 * samtools-0.1.3-20 (r276) * remove bam1_t::hash again. We need to modify the Perl API anyway to make it work with the latest SVN. * As is suggested by Tim, scan "{base}.bai" and "{base}.bam.bai" for index
adds f08c0ab * samtools-0.1.3-21 (286) * declare bam_aux_get_core() in bam.h
adds 3eb62cf Added a note to the manual. Currently SAMtools used unaligned words in several places. Although this does not cause bus errors to me, it may affect portability. Please see the "Bus error" wiki page for more information. Also thank James Bonfields for pointing this out.
adds b04b40a * samtools-0.1.3-22 (r293) * open tview in the dot-view mode by default
adds 56aa6ae added a missing header file
adds 67812fb * samtools-0.1.3-23 (r295) * fixed a critical bug in the indel caller
adds 1873431 * samtools-0.1.3-24 (r296) * another similar bug in the indel caller
adds b0ed19d Release samtools-0.1.4
adds 94bf080 * samtools-0.1.4-1 (r304) * fixed a minor bug in printing headers
adds ee493c5 Script for paired-end pileup, contributed by Stephen Montgomery.
adds 9c6f3bf * minor changes to bgzf: return NULL if fd == -1 * suggested by {kdj,jm18}@sanger.ac.uk
adds 0032bb2 * samtools.pl-0.2.0 * snpFilter
adds d5bc855 * samtools.pl-0.2.1 * fixed a typo
adds 61a8793 * in snpFilter, suppress non-SNP sites
adds fa23b4b * samtools.pl-0.2.2 * added pileup2fq
adds 4c4b723 * samtools-0.1.4-2 (r316) * pileup: cap mapping quality at 60 (by default) * pileup: always calculate RMS mapq * pileup: allow to output variant sites only
adds ce9e1dd * samtools.pl-0.2.3 * change a default parameter
adds cdd50dc * samtools.pl-0.3.0 * combine snpFilter and indelFilter
adds 6da76f1 * samtools.pl-0.3.1 * change default parameters * optionally print filtered variants
adds 6bc66a0 a little bit code cleanup
adds aa9ef2f just typo. no real change
adds e2320af fixed a typo
adds 08c9448 * samtools.pl-0.3.2 (r322) * indels and SNPs use different mapping quality threshold
adds 9360df1 * samtools-0.1.4-3 (r324) * make maqcns generate the correct call in repetitive regions. * allow filtering on mapQ at the pileup command line
adds 664c902 * samtools-0.1.4-4 (r325) * further avoid wrong consensus calls in repetitive regions.
adds 2e6c830 Unfinished
adds feb499c * added zlib-1.2.3 as razip requires that * prepare to changed back to the Makefile building system * unfinished! (will be soon)
adds 6fe3ffa * update Makefile * update INSTALL instruction
adds 831a5f9 * updated novoalign converter by Colin Hercus et al. * this version works with indels
adds 557f0dc update information...
adds 937174b * samtools-0.1.4-5 (r3310 * no change to samtools itself. Version number is increased to reflect the changes in the Makefile building system.
adds 17514ff fixed minor things in Makefile
adds a44dcfe update ChangeLog
adds 11b0656 * samtools-0.1.4-6 (r334) * do not export bam_aux_get_core() for Bio::DB::Sam because it has already been implemented in that. * this version works with the latest Bio::DB::Sam (20090612)
adds 41775b6 remove zlib for simplification...
adds 13f55c1 * no changes to samtools itself * remove zlib source codes * make RAZF reading compatible with old version of zlib * on old version of zlib, writing is not available
adds 431e646 * samtools-0.1.4-7 (r337) * bgzf.c: support mode string "wu": uncompressed output * "samtools view" support "-u" command-line option
adds 78de989 * samtools-0.1.4-8 (r338) * parse the @RG header lines and allow to choose library at the "samtools view" command line
adds 14ef69c update INSTALL
adds 63e8f52 * samtools-0.1.4-9 (r340) * added a warning to razf.c if zlib<1.2.2.1 * fixed a compilation warning * fixed a segfault caused by @RG parsing * detect NCURSES in bam_tview.c
adds 1a23a35 * samtools-0.1.4-10 (r341) * only include key APIs in libbam.a * move color-specific routines to bam_color.c * update documentations * remove the support of -q in pileup
adds 9710d19 added an example of calculating read depth
adds f35ebae nothing really
adds 0b57d1b added more comments
adds 647cc6e * samtools-0.1.4-11 (r346) * allow to select a read group at view command-line
adds d5f9862 * samtools-0.1.4-12 (r347) * added `-S' to pileup, similar to `view -S'
adds dcf3da3 * samtools-0.1.4-13 (r350) * fixed a small memory leak in pileup, caused by recent modifications
adds 9348942 * samtools-0.1.4-13 (r351) * make faidx more tolerant to empty lines right before or after > lines * hope this does not introduce new bugs...
adds 09ca4e8 * samtools-0.1.4-15 (r354) * fixed a memory leak in bam_view1(), although samtools is not using this routine.
adds cd86e7b * open a file at FTP * preliminary version
adds 7d55edb this is the header file
adds 34c4188 fixed bugs in knetfile.*
adds 3ddb394 * samtools-0.1.4-16 (r360) * report more information in index when the input is not sorted * change the behaviour of knet_seek() such that it returns 0 on success * support knetfile library in BGZF
adds 9289422 * samtools-0.1.4-17 (r361) * if a file is given on FTP, search locally for the BAM index
adds 00abd26 write changelog
adds 6dd512b * samtools-0.1.4-18 (r363) * knetfile: do not trigger network communication in FTP seek (lazy seek) * bgzf: cache recent blocks (disabled by default)
adds 356fb5e * samtools-0.1.4-19 (r364) * knetfile: report error when the file is not present on FTP
adds 3b5a80b * samtools-0.1.4-20 (r365) * download the BAM index file if it is not found in the current working directory.
adds e7c6e7a minor changes to knetfile: invalid fd equals -1 rather than 0
adds 01ddec3 reduce the chance of blocking in FTP connection
adds 8cab5e6 * samtools-0.1.4-21 (r368) * propagate errors rather than exit or complain assertion failure. Assertion should be only used for checking internal bugs, but not for external input inconsistency. I was just a bit lazy. * small memory leak may be present on failure, though
adds d37a338 * samtools-0.1.4-22 (r369) * in pileup, optionally print E2 and U2 * remove the debugging code in bam_aux_get() (Drat!)
adds d9f7293 Introduced LIBPATH variable so this could be overridden to allow samtools to build correct at the Broad.
adds 4120469 update documentation
adds 21cb882 * samtools-0.1.4-23 (r372) * keep header text if "view -t" is used (by Gerton)
adds 9f30c9b Release samtools-0.1.5
adds b276050 Release samtools-0.1.5a (for compatibility with Bio::DB::Sam)
adds d47b585 Release samtools-0.1.5b (BUG! so embarrassing!)
adds 63a8030 Release samtools-0.1.5c (fixed a bug in piping)
adds 42e48c7 * samtools-0.1.5-1 (r390) * removed useless _IOLIB in bam.h. This should cause no change at all. * added bam_lite.c for light-weight BAM reading
adds 67392b8 * samtools-0.1.5-2 (r391) * do not show a blank screen when no reads mapped
adds 932483e Remove the warning in tview
adds 0a5854b * samtools-0.1.5-3 (r393) * knetfile now supports HTTP (no proxy at the moment) * fixed a potential issue in knetfile on opening ordinary file, although I have not seen the sideeffect so far.
adds ebb5378 * samtools-0.1.5-4 (r394) * http_proxy support in knetfile library (check http_proxy ENV)
adds f8941ae * samtools-0.1.5-5 (r395) * added bam_pileup_file() and removed bam_lpileup_file()
adds 286c75f * move bam_lite.c to bam-lite * copy bam.h to bam-lite
adds 5ad642a * samtools-0.1.5-6 (r402) * fixed compiling error when "-D_USE_NETFILE" is not applied * improve portability to MinGW
adds 5a0f00a * samtools-0.1.5-7 (r403) * fixed a bug in kseq.h for binary files (text files are fine)
adds dc15010 * samtools-0.1.5-8 (r404) * compatible with PDCurses
adds a5a8f24 * samtools-0.1.5-9 (r405) * improved the compatibility with PDCurses a little bit
adds 33c76f7 Sorry. The old Makefile is for PDCurses...
adds 011fa10 * samtools-0.1.5-10 (r407) * implemented bam_aux_del() to remove a tag * fillmd: generate the NM tag * fillmd: cmd interface improvement
adds 030a404 * samtools-0.1.5-11 (r408) * force to overwirte existing MD if it is different from the one calculated from fillmd. * bgzf.c: improved the compatibility with Windows headers
adds 23e4a70 do not include knetfile.h when _USE_KNETFILE is not defined
adds 0cc4f35 Implemented Boyer-Moore search in the kstring library.
adds cda19b9 fixed a compiling error (thank Ken for fixing it)
adds 941542d * samtools-0.1.5-12 (r415) * FLAG now can be in HEX
adds 6f6733c * samtools-0.1.5-17 (r416) * support import/export SAM with string tags
adds 1ce5cbd * samtools-0.1.5-14 (r417) * more help in "samtools view" due to the recent changes.
adds 1e11e2b skip @header lines in SAM
adds f87674c * samtools-0.1.5-15 (r419) * in sam_open(), return NULL when the file cannot be opened. * make wgsim_eval.pl more robust to imperfect SAM * add "unique" command to samtools.pl
adds d89ec29 do not set "read 1" if reads are not mapped in the PE mode of maq
adds 9bd8cd7 * samtools-0.1.5-16 (r421) * in view and pileup, load header from FASTA index if the input is SAM.
adds 8a9ee84 * samtools-0.1.5-17 (r422) * fixed a but in knetfile.c when seek type is not SEEK_SET * write an empty BGZF block to every BGZF file * check BGZF EOF marker in bam_header_read() * update ChangeLog
adds a62dcaa convert BLAT psl to SAM.
adds 2ec7794 * samtools-0.1.5-18 (r423) * output additional information in pileup indel lines, for the purepose of debugging at the moment * in tview, optionally allow to treat reference skip as deletion
adds 2038708 compatible with Windows binary files
adds 0440771 * samtools-0.1.5-19 (r426) * fixed a bug caused by recent modifications. Sorry.
adds 70e9232 * samtools-0.1.5-20 (r427) * MinGW support. At least SAM<->BAM conversion is working. Other functionality are not tested at the moment. * zlib headers and Windows version of libz.a are included in win32/
adds 3c951a3 simplify MinGW Makefile
adds a3f9235 * samtools-0.1.5-21 (r428) * knetfile.c is now compatible with mingw-winsock
adds 3fc256b add comments
adds e25b460 replace the GnuWin32 version of libz.a with my own build with MinGW.
adds 5541801 * samtools-0.1.5-22 (r432) * faidx: fixed compitability issue with _WIN32 * razf: fixed potential compitability issue with _WIN32 * PDCurses support in Windows
adds 218ac0c * tried to fixed the buggy FTP random access in Windows. FAILED. * anyway, MinGW seems to have problem with "%lld".
adds de9c95e * samtools-0.1.5-23 (r434) * in tview, press 'r' to show read names rather than sequences
adds ae8b3d2 * samtools-0.1.5-24 (r435) * fixed a typo
adds 1953023 fixed two minor bugs (suggested by Tim M Storm)
adds 3a42c37 fixed a SERIOUS bug in setting 0x20 flag
adds 4fad92d * samtools-0.1.5-25 (r436) * in flagstats, do not report singletons if both ends are unmapped
adds 53071bf Change copyright notices now that MIT has approved open source distribution.
adds c411144 * samtools-0.1.5-26 (r442) * replace RSA Inc md5.* with ones under permissive lincense * fixed a bug in detecting unsorted bam in pileup
adds a8c8618 * samtools-0.1.5-27 (r443) * SEQ and QUAL can be "*" * parse CIGAR "=" and "X" as "M"
adds 54f5a85 * samtools-0.1.5-28 (r444) * bug in "merge -n"
adds c92c84d *
adds e641ee5 * samtools-0.1.5-30 (r447) * fixed a bug in bam_aux_get(): 'A' is not checked
adds dec171a * samtools-0.1.5-31 (r448) * fixed an issue when the last CIGAR is I or D
adds 140d53d * samtools-0.1.5-32 (r449) * fillmd: fixed a bug in modifying MD/NM tags * in import, give a warning if the read is aligned but there is no CIGAR.
adds da9fd68 * samtools-0.1.5-33 (r450) * fixed a bug in bam_color.c (on behalf of Nils Homer)
adds 521aa49 * samtools-0.1.5-34 (r451) * applied the patch by John * improved the help message a little bit
adds 0746c10 Release samtools-0.1.6
adds a871942 Return NULL from _razf_open() (and hence razf_open()/razf_open2()) when opening the file fails.
adds c18ba0d * samtools-0.1.6-2 (r457) * get rid of three assert() in bam_sort.c
adds 5edf841 * samtools-0.1.6-2 (r458) * added more interface to faidx (by Nils) * updated documentation
adds 8de1cc9 * samtools-0.1.6-4 (r459) * make sort output the result to stdout when -o is in use
adds b9014ed fixed a formatting issue
adds d56f285 * samtools-0.1.6-5 (r462) * Added knetfile support in razf and faidx (on behalf of Petr Danecek)
adds 32c42f6 A bug fix, "samtools view" is now working again.
adds 2713255 Suppress bgzf_check_EOF() messages when reading from a pipe, as there is no way to seek on a pipe and the messages always appear.
adds bf67509 * samtools-0.1.6-6 (r466) * do not crash calmd when some sequences are absent from the reference.
adds 5078180 Changed the mode for newly created files to 0666. This allows less strict permissions with umask properly set (e.g. 0002 vs. 0022).
adds d8f714c * samtools-0.1.6-7 (r468) * make merge stable
adds daf3efd * samtools-0.1.6-9 (r469) * refactor bam_fetch() for Python binding. On behalf of Leo Goodstadt.
adds 089233f * samtools-0.1.6-9 (r470) * make knetfile.c compatible with MinGW (thank Martin Morgan for the patch)
adds a2465b1 Fixed minor bugs in novo2sam.pl (on behalf of Ken Chen and Colin Hercus)
adds d70b59e Clarify the meaning of a region like "chr2:1,000,000".
adds 8e17ff7 Bug fix - faidx on RAZF compressed files now working.
adds 9dd911d Removed the offending knet_seek message.
adds 020baf3 Unfinished modification. Please do not use this revision...
adds d0cd897 Added the sam2vcf.pl script.
adds b05dd87 * samtools-0.1.6-11 (r477) * fixed a bug due to recent change in bam_index.c (thank Nicole Washington for the patch)
adds 0cccdf5 * samtools-0.1.6-12 (r478) * fixed a bug in the indel caller
adds 4c2687f * samtools-0.1.6-13 (r479) * merge: optionally use file names as RG tags
adds 963fc75 added a small unitity to parse SRA XML files
adds 228debe * samtools-0.1.6-14 (r480) * rmdup is now RG aware
adds d084580 * samtools-0.1.6-15 (r482) * rewrite rmdupse * rmdupse is now library aware
adds 8bee1f1 * samtools-0.1.6-16 (r483) * unify the interface of rmdup and rmdupse * a new bug found in rg2lib(). Have not been fixed yet.
adds 56ae21c * samtools-0.1.6-17 (r484) * fixed a memory leak in rmdupse * fixed a bug in parsing @RG header lines * test rmdup in examples/
adds d410ecb
adds ef49247
adds bb9a823 Now possible to merge multiple HeaderDict dictionaries
adds d0e30ee * This revision is SERIOUSLY BUGGY. Please NOT use it. * Start to incorporate header parsing from Petr Danecek
adds ed9cedc * BUGGY VERSION. Please NOT use it. * Fixed a minor bug, but the major bug is still there.
adds b188ebc * BUGGY VERSION * improved the interface a bit * bug unfixed
adds 039d3c2 * BUGGY VERSION * fixed a minor bug
adds 2081e53 Added sam_header_line_free call for sam_header_parse2
adds 87d9ea7 * samtools-0.1.6-18 (r493) * fixed the bugs due to improperly incorporating Petr's header parser * a little code clean up in sam_header.c
adds 321c3f4 * samtools-0.1.6-19 (r494) * allow to convert Illumina quality (64 based) to the BAM quality
adds a7dfcd3 * samtools-0.1.6-21 (r508) * fixed a potential bug in the indel caller towards the end of a chromosome
adds ec5db83 * samtools-0.1.6-22 (r509) * forget to fix a similar problem in glfgen
adds 67b0f11 Release samtools-0.1.7 (r510)
adds 45dd4bc Fixed a bug in compiling razip
adds 9c60e50 Update Makefile.mingw for the same reason
adds 13a7326 Format 'c'-encoded auxiliary fields correctly, as *signed* integers.
adds 9215c09 * samtools-0.1.7-1 (r515) * report an error when .fai contains duplicated names, instead of segfault
adds d8137f3 another example program
adds 185ac16 Index files should be opened in binary mode, not text mode.
adds 794e74d Also clean *.exe (for Cygwin users using this makefile).
adds 4234ca8 Put libraries at the end, so they can resolve references from libbam.a as well, even with old-fashioned linkers.
adds 2104bef * samtools-0.1.7-2 (r520) * fixed a few issues with compilation in Windows (on behalf of John) * choose a random base as the consensus (for population genetics studies)
adds e9625b3 * samtools-0.1.7-3 (r521) * calmd: optionally mask matching bases as N
adds 83f055f * samtools-0.1.7-4 (r522) * fixed a bug in "view -r" * added a new option "view -R" to read required read groups from a file
adds 2a42471 Fix a bug in compiling bgzip: this also needs knetfile.o when _USE_KNETFILE is defined. Also introduce $(KNETFILE_O) which can be set to empty to facilitate non-knet builds.
adds 8bff7a4 Depend on libbam.a rather than the phony target, so that samtools is not unnecessarily rebuilt every time. Also clean bgzip.
adds 2bcc5f0 Allow tabs in the CO header field
adds af44e7f Small fix in VCF format: dot for the empty INFO field
adds 1602fce Fixed a bug in knet_seek
adds 6971381 * samtools-0.1.7-5 (r528) * further add new consensus generation strategy
adds 5f226a4 Put the right filename in the error message.
adds 6ad0dc5 * samtools-0.1.7-6 * fixed a bug in faidx
adds 47a7af0 Added VCF header
adds 7e56a16 Added the -d option to limit maximum depth for indels.
adds 8443a81 Added possibility to specify a custom column title for the data column
adds cf4f8cb added a hidden option in pileup to output the base position (for Erin)
adds d04b701 Print an error for pileups in simple format
adds 88abd40 Fixed filtering of SNPs near indels. Added min indel and SNP quality filter.
adds 2378a4e Updated export2sam.pl by Chris Saunders from Illumina.
adds b3a8c55 Improved efficiency of header parsing
adds ce728f5 Improve the invalid 'BAM\1' magic number error message, and also print it when no bytes can be read from the alleged BAM file, e.g., in the common user error case when a SAM file has accidentally been supplied.
adds 92c9c2e Added possibility to select indels only and fixed a bug in reporting homozygous indels.
adds afda9d0 Fixed the order of sequences in the header
adds 316dda0 Speedup with -i, no need to query the reference all the time
adds bef0453 More descriptive message for space separated tags
adds 9c833e8 Added the possibility to print or not to print the reference allele
adds 6a90b50 Added a note about the indels coordinates
adds 4887e63 Initial release on behalf of Aylwyn Scally
adds 78b65b0 * samtools-0.1.7-7 (r584) * ported tabix BGZF to samtools * flush BGZF after writing the BAM header and between alignment boundaries
adds 67e2782 * samtools-0.1.7-8 (r585) * speed up "view"
adds de48a5e * samtools-0.1.7-9 (r586) * added "reheader" to replace the BAM header
adds 936ebcc * samtools-0.1.7-10 (r587) * added iterator interface for bam_fetch (ported back from tabix)
adds fe524d8 * samtools-0.1.7-11 (r588) * ported a few improvements from tabix back to samtools
adds bc85112 * samtools-0.1.7-12 (r589) * added iterator-like APIs for pileup
adds a9699b0 * samtools-0.1.7-13 (r590) * added mpileup APIs. No compiling errors, but not tested at all. It is late.
adds aee93c8 * samtools-0.1.7-14 (r591) * elementary multi-way pileup. More testing and more functionality to be done.
adds 4967051 * samtools-0.1.7-15 (r592) * fixed a few minor memory leaks in the new pileup code * improved the functionality of mpileup
adds a958954 rename iterf as iter
adds 64b94f9 fixed a bug for unmapped sequences in indexing
adds bddd8e7 * samtools-0.1.7-16 (r595) * write additional information to bam index
adds adefe52 * samtools-0.1.7-17 (r596) * also keep the number of coor-less reads in the index file
adds e3532f8 added Makefile targets to compile shared/dynamic library
adds 6235d86 minor fix. No actual effect.
adds ea7a6d0 change printf() to puts in exporting
adds 7aac246 fixed a minor bug in indexing
adds a5adc91 fixed a minor bug in idxstats
adds 5ccaa67 * samtools-.1.7-18 (r605) * fixed an issue when a deletion and mismatch occur at the same time and the base quality is higher than 40 (if -I40).
adds 9c7e809 removed a debugging example
adds efa4a10 * samtools-0.1.7-r607 * improved the genotype accuracy for indels * use the SOAPsnp model for SNP calling by default.
adds 961c3fe * make tview more friendly * a temporary remedy for an issue in indel calling
adds 3d80bf0 make pileup work with CIGAR with I/D at the beginning or in the end
adds 7541523 change the command line option of pileup
adds 876f043 fixed a bug in sorting when output to stdout (by Peter Chines)
adds 3f948da fixed a compiling issue for Windows
adds aecbff7 Release samtools-0.1.8
adds 8b0f98e * samtools-0.1.8-1 (r615) * allow to get mpileup at required sites
adds 921db5e * added mutli-sample framework. It is not working, yet. * improved the mpileup interface
adds 7795f54 * samtools-0.1.8-2 (r617) * allele frequency calculation apparently works...
adds d73a1b3 * preliminary multisample SNP caller. * something looks not so right, but it largely works
adds d763698 * samtools-0.1.8-3 (r627) * multi-sample snp calling appears to work. More tests needed.
adds a11820a calculate posterior allele frequency
adds 7135585 added an alternative prior
adds dc7a003 added the format column
adds 0c48be0 another minor fix to mpileup
adds e23eb12 posterior expectation FINALLY working. I am so tired...
adds d742c10 minor tweaks
adds be66702 minor changes
adds fb9ec86 * samtools-0.1.8-6 (r638) * skip isnan/isinf in case of float underflow * added the flat prior * fixed an issue where there are no reads supporting the reference
adds 7f8bb28 * samtools-0.1.8-7 (r639) * fixed the reference allele assignment
adds cb946d1 NOT ready yet. Going to make further changes...
adds 82c492c supposedly this is THE correct implementation, but more testing is needed
adds 850bfd5 * fixed a STUPID bug, which cost me a lot of time. * I am going to clean up mcns a little bit
adds 084a278 * samtools-0.1.8-8 (r644) * mpileup becomes a little stable again * the method is slightly different, but is more theoretically correct * snp calling is O(n^2) instead of O(n^3)
adds 7eaf231 Generate binary VCF
adds 6718447 * samtools-0.1.8-9 (r649) * lossless representation of PL in BCF output
adds ad3f2c5 fixed a bug
adds 72c7831 fixed a bug in bcf reader
adds 292dcee fixed a memory leak
adds dcf96f6 missing a column in VCF output...
adds 6ff460f * fixed a bug * treat ambiguous ref base as the fifth base
adds b443abe * samtools-0.1.8-10 (r658) * fixed a bug in bam2bcf when the reference is N
adds 3fbc368 fixed another minor bug
adds fd18746 move bcftools to samtools
adds 6f1c722 fixed compilation error
adds 24d22cf added more examples
adds 4ff943f spec
adds c0490a6 * allow to set min base q * fixed a bug in mpileup -u
adds a90c2f6 * added prelimiary VCF parser (not finished) * change struct a bit
adds e09919c unfinished vcf parser
adds 6df2741 minor
adds 95882d9 * the code base is stablized again. * I will delay the vcf parser, which is quite complicated but with little value for now
adds cbe4205 * samtools-0.1.8-11 (r672) * collect more stats for allele balance test in bcftools (not yet)
adds 7ee053d Fisher's exact test
adds 6d8992d * Special functions: log(gamma()), erfc(), P(a,x) (incomplete gamma) * Not using Numerical Recipe due to licensing issues
adds f27c5d3 * bcftools: add HWE (no testing for now) * record end dist in a 2x2 table, not avg, std any more
adds ae50b36 reimplement incomplete gamma functions. no copy-paste
adds 2bd87be * test depth, end distance and HWE
adds 119f18a perform single-tail test for ED4
adds ed5305b help messages
adds 94027d8 * improved kstring (added kstrtok) * removed the limit on the format string length in bcftools * use kstrtok to parse format which fixed a bug in the old code
adds 8632908 * fixed a bug in kstrtok at kstring.c * preliminary VCF parser (not parse everything for now) * improved view interface
adds e5d4bf8 * parse PL * fixed a bug in parsing VCF
adds ce14f3d do not print refname if file is converted from VCF
adds 7ddef21 fixed an issue in parsing integer
adds b65b44f * a numerically stable method to calculate z_{jk} * currently slower than the old method but will be important for large sample size * in principle, we can speed up for large n, but have not tried
adds d776257 faster for large sample size (in principle)
adds af4483b use float for QUAL
adds ac10f1f * write a little more VCF header * concatenate BCFs
adds b6f550e allow to read the prior from the error output. EM iteration is working.
adds 5c4ef83 added revised MAQ error model
adds 6dc53c5 * use the revised MAQ error model for mpileup * prepare to remove the independent model from mpileup
adds 63af098 remove VCF output in mpileup
adds d14782f * samtools-0.1.8-12 (r692) * group data by samples in "mpileup -g"
adds 05cb7b5 print QUAL as floating numbers
adds 998b354 change the default correlation coefficient
adds 4c6157a added regularized incomplete beta function
adds f69357a * samtools-0.1.8-13 (r698) * perform one-tailed t-test for baseQ, mapQ and endDist
adds d8179b7 fixed a bug in calculating the t statistics
adds 082c52f * rename vcfout.c as call1.c * prepare to add two-sample comparison
adds 3f13738 z' and z'' can be calculated
adds 390bbfb preliminary contrast variant caller
adds 036b8f5 Utilities for processing VCF
adds 7ef8272 more commands for my own uses
adds 6418571 Write the correct ALT and PL in the SNP calling mode.
adds b62e611 Do not compile _BCF_QUAD by default
adds 39eb148 * fixed bugs in parsing VCF * parser now works with GT/GQ/DP/PL/GL
adds eacb9ea fixed another problem
adds 018b503 SNP calling from the GL field
adds 955605d * changed 3.434 to 4.343 (typo!) * fixed a bug in the contrast caller * calculate heterozygosity
adds c219160 quite a lot changes to the contrast caller, but I still feel something is missing...
adds d4c6e3a * samtools-0.1.8-13 (r715) * fixed a bug in identifying SM across files * bcftools: estimate heterozygosity * bcftools: allow to skip sites without reference bases
adds 0b3bad7 Add svn:ignore properties listing the generated files. (Except for *.o, which we'll assume is in global-ignores.)
adds 07c8d11 Add svn:ignore properties for generated files that don't appear in "make all".
adds addab0d * aggressive gapped aligner is implemented in calmd. * distinguish gap_open and gap_end_open in banded alignment * make tview accepts alignment with heading and tailing D
adds 75c9ea6 minor changes. It is BUGGY now!
adds cd65d35 fixed a bug in realignment
adds cac5f70 fixed a minor issue
adds 221f82f fixed a bug in realignment
adds 112a5a1 dynamic band width in realignment
adds 7c51db2 * convert BCF to QCALL input
adds 51f0141 * added varFilter to vcfutils.pl * reimplement realn(). now it performs a local alignment * added cap_mapQ() to cap mapping quality when there are many substitutions
adds 6cda28b * samtools-0.1.8-14 (r727) * allow to change the capQ parameter at the command line
adds 2cbbde8 * fixed a bug in razip: -c will delete the input file * copy tabix/bgzip to here
adds cdfe597 * fixed a bug in capQ * valgrind identifies a use of uninitialised value, but I have not fixed it.
adds 4e4e3fd fixed a bug in indexing
adds 4fe4b27 * put n_smpl to "bcf1_t" to simplify API a little
adds f418206 * added comments * VCF->BCF is not possible without knowing the sequence dictionary before hand...
adds d11a5b1 hapmap2vcf convertor
adds 1f92eaf convert UCSC SNP SQL dump to VCF
adds 41c6c24 improve qstats by checking the alleles as well
adds be38544 * merge files region-by-region. work on small examples but more tests are needed.
adds 8ad43dd 0 is a successful return value from bam_read1(). (In practice, it never returns 0 anyway; but all the other callers treat 0 as successful.)
adds ca535cf When bam_read1() returns an error (return value <= -2), propagate that error to bam_iter_read()'s own return value. Similarly, also propagate it up to bam_fetch()'s return value. Previously bam_fetch() always returned 0, and callers ignored its return value anyway. With this change, 0 continues to indicate success, while <= -2 (which can be written as < 0, as -1 is never returned) indicates corrupted input.
adds bdee6f5 * samtools-0.1.8-15 (r379) * allow to change capQ parameter in calmd
adds 30f48c3 Add bam_validate1().
adds ccd9871 Use bam_validate1() to detect garbage records in the event of a corrupt BAI index file that causes a bam_seek() to an invalid position. At most one record (namely, the bam_iter_read terminator) is tested per bam_fetch() call, so the cost is insignificant in the normal case.
adds 5008027 Abort if merge -h's INH.SAM cannot be opened, just as we abort if any of the IN#.BAM input files cannot be opened.
adds 9e59c3b ...
adds 66ecc9e A little code cleanup. Now the forward and backback algorithms give nearly identical P(x), which means both are close to the correct forms. However, I have only tested on toy examples. Minor errors in the implementation may not be obvious.
adds 8587a0e More comments. This version seems working, but something is a little weird...
adds e32b6f0 * fixed that weird issue. * the banded version is NOT working
adds 1027e43 fixed a bug in banded DP
adds 3f2413d more comments
adds 0f49072 improve numerical stability
adds 35370d9 Implement the glocal HMM; discard the extention HMM
adds 314676c Convert phredQ to probabilities
adds 0a45952 minor
adds 4c8358d prob_realn() seems working!
adds d8d3ad5 minor changes
adds 5efaf4a this is interesting. multiplication is much faster than division, at least on my Mac
adds 48a7322 I was trying to accelerate ka_prob_glocal() as this will be the bottleneck. After an hour, the only gain is to change division to multiplication. OK. I will stop.
adds bed4b3d round to the nearest integer
adds 81cfb5b mark samtools-0.1.8-16 (r759)
adds e97b0dd * samtools-0.1.8-17 (r760) * the default gap open penalty is too small (a typo) * added comments on hmm_realn * Java implementation
adds 31ef055 I am changing the gap open probability back to 0.001. It seems that being conservative here is a good thing...
adds 82e06ed * vcfutils.pl qstats: calculate marginal ts/tv * allow to call genotypes at variant sites
adds dda27af * samtools-0.1.8-18 (r763) * added bcftools manual page * minor fix to mpileup and view command lines
adds fdeef62 Convert VCF output of "bcftools view -bgcv" to a valid VCF file
adds 535d36c * removed a comment line in kaln.c * vcfutils.pl fillac works when GT is not the first field
adds a77f3af added filter for samtools/bcftools genetated VCFs
adds 0329376 * vcfutils.pl: fixed a typo in help message * added APIs: bcf_append_info() and bcf_cpy() * calculate adjacent LD
adds bd35dfe forget to add the key file
adds b28a2f5 a minor change
adds 5ffbb83 * a minor fix to the -L option * add ldstats to vcfutils.pl
adds 30d4223 improve the LD statistics
adds 33e4331 added another toy example
adds eba7ecb * Minor code changes. No real effect. * change quality to 30 in toy.sam
adds f53cb16 Add the relevant filename or region to error messages, and cause a failure exit status where appropriate. Based on a patch provided by Marcel Martin.
adds 8a994c1 remove local realignment (probabilistic realignment is still there)
adds 0993e91 * samtools-0.1.8-19 (r777) * integrate mpileup features to pileup: min_baseQ, capQ, prob_realn, paired-only and biased prior
adds 253dbf0 * samtools-0.1.8-20 (r778) * speed up pileup, although I do not know how much is the improvement
adds 6ee6fd6 improve pileup a little bit
adds c9a9c27 * samtools-0.1.8-21 (r780) * minor speedup to pileup
adds 1c7f804 * samtools-0.1.8-22 (r781) * made BAQ the default behavior of mpileup * updated manual * in merge, force to exit given inconsistent header when "-R" is not in use.
adds 3bedbd7 fixed a silly bug in pileup
adds ac32543 Release samtools-0.1.9 (r783)
adds 88253dc acknowledge Petr and John who have greatly contributed to the project.
adds f221655 Optionally output "DP", the individual read depth
adds 896d270 * samtools-0.1.9-1 (r786) * samtools: optionally perform exact test for each sample
adds 9114242 * samtools-0.1.9-2 (r787)
adds 15a0c37 Added -b option: read file names from a file
adds 168ad09 Separate kaln and kprobaln as I am preparing further changes. At present, the results should be identical to the previous.
adds 48c1052 fixed a minor problem in the example coming with kprobaln.c
adds 98946f7 for backup. no effective changes
adds df7cada * this revision is UNSTABLE
adds 2d2be1e Revert to r790. The recent changes are not good...
adds 0bb4884 prepare for the indel caller. It is not ready yet.
adds 53afc90 fixed a few bugs in the indel caller. Probably there are more.
adds 917ed8c indel calling is apparently working, but more information needs to be collected
adds 599bea1 * samtools-0.1.9-2 (r797) * mpileup: indel calling seems to be working
adds 4bb71ff Incorporate patches by Marcel Martin for read counting.
adds 0917f66 fixed a silly bug in the indel caller
adds 42a3880 fixed another silly bug in mpileup's indel caller
adds e2d4caa * samtools-0.1.9-4 (r801) * fixed a minor issue in printing indel VCF
adds ff6d24e * samtools-0.1.9-5 (r802) * relax tandem penalty. this will be made a command-line option in future.
adds e561d6e * samtools-0.1.9-6 (r803) * mpileup: apply homopolymer correction when calculating GL, instead of before * bcftools: apply a different prior to indels
adds ed191cc * samtools-0.1.9-7 (r804) * fixed a bug in the gap caller
adds 004badb added a double-hit filter to avoid overestimated indel likelihood
adds e609145 bcftools: compute equal-tail (Bayesian) credible interval
adds 165f1d8 * samtools-0.1.9-8 (r807) * collect indel candidates only from specified platforms (@RG-PL) * merge varFilter and filter4vcf in vcfutils.pl
adds 0df4d11 minor change to makefile
adds 1a1147a * samtools-0.1.9-8 (r809) * fixed a bug in the indel caller
adds 3769ac2 * do not use reads containing too many mismatches for indel calling * fixed a trivial bug in case of multi-allelic indels
adds 6c4bde5 use zlib for direct reading when BCF_LITE is in use
adds 141c7b5 fixed a typo
adds fe9d679 * prepare to replace kaln with kprobaln in realignment
adds 29e8a5f * samtools-0.1.9-9 (r810) * use forward, instead of viterbi, for realignment * realignment is now quality aware
adds e252a35 effectively revert to the viterbi version. The forward realignment gives too many false positives.
adds b79e085 * samtools-0.1.9-10 (r816)
adds b0ae0ca * samtools-0.1.19-11 (r817) * only initiate indel calling when 0.2% of reads contain a gap
adds bf8b35c * samtools-r818 * for indel calling, do two rounds of probabilistic realignments
adds 35dc3eb * samtools-0.1.9-13 (r819) * fixed a bug in pileup given refskip
adds 6bc810f * samtools-0.1.9-14 (r820) * penalize reads with excessive differences in indel calling
adds 21981f7 * samtools-0.1.9-15 (r821) * calmd: write BQ * skip realignment if BQ is present
adds 95b7e2d * samtools-0.1.9-16 (r822) * keep the raw depth because in indel calling, DP4 may be way off the true depth
adds 36cee82 * samtools-0.1.9-r823 * the BQ tag is now 64 shifted, not 33 shifted
adds f560d9a * samtools-0.1.9-17 (r824) * added command line options to change the default parameters in indel calling * update the manual
adds a27cb2a * samtools-0.1.9-18 (r825) * change the behaviour of calmd such that by default it does not change the base quality
adds 796a36e remove ZQ if both BQ and ZQ are present
adds 449c4e4 bcftools: allow to skip indels
adds fb0ba93 update version information: samtools-0.1.9-20 (r828)
adds 624c76e Release samtools-0.1.10 (r829)
adds 4c8c9df * samtools-0.1.10 (r831) * initial MNP caller
adds 3d0fb2f minor change to how seqQ is applied
adds 0735c4c fixed a bug in printing MNPs
adds a499d2a * samtools-0.1.10-4 (r834) * fixed a silly bug in printing MNP * restrict to at most 1 alternative allele
adds 8da27db * modify the filtering rule: also filter SNPs around filtered indels * added MNP filter
adds 8757ce4 * samtools-r836 * initiate MNP realignment when the MNP has at least 0.2% frequency (otherwise too slow)
adds 4ec3d44 Apply a patch by Rob Davis, which improves fault detection.
adds ea1bf85 * samtools-0.1.10-6 (r839)
adds 30004e9 * samtools-0.1.10-4 (r840)
adds 543a65c * samtools-0.1.10 (r841) * fixed a bug in pileup when the first CIGAR operation is D * fixed a bug in view with range query
adds 1443ba1 When merging BAM headers, compare the list of target reference sequences strictly (and fail/abort if there is a mismatch), but allow one list to be a prefix of the other. (i.e., check that the lists are identical up until the shorter runs out, and add the excess targets from the longer to the output.)
adds c957fcd In merging, if -R is specified, do not abort if the sequence dictionary is different.
adds 7943d9b * samtools-0.1.10-9 (r844) * added the "folded" or reference-free mode for variant calling
adds 604b0bc Release samtools-0.1.11
adds 3051bc3 forget to change the version information
adds 22e4ba8 fixed a typo/bug in r^2 computation
adds 1a302a6 * fixed a memory violation * added splitchr to vcfutils.pl
adds ad08966 fixed a memory leak in bam_fetch()
adds 82797ab * samtools-0.1.11-1 (r858) * fixed a bug in mpileup which causes segfaults * bcftools: do not segfault when BCF contains errors
adds 07f8f0c Release samtools-0.1.12
adds e484b71 a possible fix to DP4=0,0,0,0; have not tested, but should have no side-effect
adds 5babaae Release samtools-0.1.12a
adds 8af173e more informative error message
adds 765ae9e * remove "-f". Instead always compute consensus quality * increase the upper limit of quality
adds 9c614e7 vcf->fastq
adds 51ffe3e Fixed a compiling error when knetfile is not used.
adds af97892 bring back the windows support
adds 9c6a90d In ksprintf(), change "%lf" and "%lg" to "%f" and "%g", respectively. According to the manual page, this change is valid. However, MinGW seems to interpret "%lf" as "%Lf".
adds cb83f48 added a warning for the Windows version
adds 8a29cb3 fixed a bug in vcf2fq
adds 6ed91e9 * samtools-0.1.12-1 (r873) * added a switch to allow anomalous read pairs in calling
adds 1bb8e1e a spelling error..
adds d062f8f * samtools-0.1.12-2 (r877)
adds 2a95d0b Make sure that the GT genotype field is the first
adds ce00ece * fixed a minor issue in printing VCFs * write bcftools specific INFO and FORMAT in the header
adds 8937e7f drop bcf-fix.pl as it is redundant by the latest changes
adds 5f5ed24 compute max SP and max GQ from sample genotypes
adds 7d93d10 * samtools-0.1.12-4 (r884) * fixed a long-existing flaw in the INDEL calling model
adds bc2ecad Fixed the VCF header to pass validation
adds ec8d07a (Arguably) improved the indel caller a tiny bit for lowCov data.
adds 75777ee * samtools-0.1.12-6 (r887) * added a hidden option -E to mpileup/calmd. -E triggers an alternative way to apply BAQ.
adds 8e0cda9 When -B is applied to mpileup, still use paired reads only unless -A is flagged.
adds c1e9248 * samtools-0.1.12-12 (r889) * set mapQ as 20 if it equals 255
adds f0b7a68 * samtools-0.1.12-9 (r891) * allow to call SNPs from a subset of samples
adds ceff94a System libraries go *after* user libraries in link commands, because the user libraries may themselves have dependencies that are satisfied by the system libraries. It's not rocket science!
adds 3b4c5ef Fixed a typo in read_samples
adds f369cdf added ST
adds 83269f1 sorry. It is SP not ST
adds c5d9a22 * samtools-0.1.12-10 (r896) * allow to exclude read groups in mpileup
adds 5f33ece move bam_nt16_nt4_table[] from bam_maqcns.c to bam_md.c
adds 5a38c3f Skip sites with unknown ref
adds 0962489 fixed two minor bugs in Fisher's exact test
adds d1643d6 * fixed a rare memory issue in bam_md.c * fixed a bug in indel calling related to unmapped and refskip reads
adds ac136c5 * avoid a segfault when network connect fails * update INSTALL * fixed a bug in tview on big-endian by Nathan Weeks
adds fee22b6 * fixed an out-of-boundary bug * improved sorting order checking in index
adds 8da8f72 fixed a typo in the VCF header
adds 1ee2aff Prevent division by zero
adds 06021e3 finished VCF->BCF conversion
adds c8e59c5 * automatically fix errors in GL * output unrecognized FORMAT as "."
adds 8c132db more meaningful BAM truncation message
adds 205b696 added "const" to bcf_p1_cal()
adds 7251efa added the phase command
adds 29e08d7 update the BCF spec
adds 27eec65 * change the order of PL/GL according to the latest VCF spec * change the type of SP to int32_t
adds fe25084 * put version number in bam.h * write version to BCF * in phase, change the default -q to 37 * output a little more information during phasing
adds 213027e * 0.1.12-r924:126 * fixed a bug in phase (due to recent changes) * fixed a bug in vcf2fq
adds 6213209 minor changes to a heuristic rule
adds 72b2e93 * optionally drop phase ambiguous reads * write vcf format 4.1 instead of 4.0
adds 727b8c1 Release samtools-0.1.13 (r926:134)
adds f528e7d added the haploid mode
adds 9cbf642 export2sam.pl-2.3.1, provided by Chris Saunders from Illumina Inc.
adds d382711 * allow to change the compression level in BAM output * use compress level 1 in sorting * association test * concatenate BAMs * allow to threshold on max depth in INDEL calling
adds 082f868 forget to add this file
adds 8ef16f0 Release samtools-0.1.14 (r933:170)
adds 674ffee * added BED support to samtools view and mpileup and bcftools view * ML estimate of allele frequency in two groups * better error message given inconsisten RG labels * compute all-pair r^2
adds 993e30c * synchronize bgzf in tabix and in samtools * fixed a severe bug in bedidx.c
adds 1cd91e7 Added an example of using mpileup
adds c72cba5 fixed a few typos in comments
adds e6ca3f8 added quality filtering
adds 50706be * added bam_verbose global variable * fixed a bug when grouping reads in mpileup (due to recent changes) * do not validate SAM header * estimate genotype frequency * added HWE test back, but with a different method
adds 19bf588 Release samtools-0.1.15 (r949:203)
adds 0f5ce5a * Added Brent's method for frequency estimate * Added likelihood ratio test for HWE and association
adds ce2a057 * fixed a bug in bedidx: input BED not sorted * make bcftools a little bit more robust given wrong inputs * perform posterior-chi^2 by default
adds ea89c55 Added the support for the new SAM/BAM type "B"
adds d452c6f fixed a bug in merge
adds 8ec3e2c Release samtools-0.1.16 (r963:234)
adds c350a57 Removed the pileup command
adds 80658e4 * 0.1.16-dev (r969:252) * faidx/view: smarter way to parse a region string * index: more rigorously check the sorting order * Makefile: added -s to ar * bcftools: compute 2-degree P-value by default * bcftools: compute the ML estimate of the allele count
adds 4d48006 fixed a bug caused by a recent patch
adds 3384f6c Release samtools-0.1.17
adds ef04d52 fixed a bug in bam_plcmd.c
adds 5329dbb for WIN32 compatibility
adds 23e43ef support trio indels
adds d195bcf subsampling read pairs
adds 2c05c1d allow to set seed in view-subsampling
adds cb5f449 * bugfix in index: large memory when a read pos is 1 * bugfix in BAQ: incorrect probability (rare) * compute variant distance bias (commited by Petr) * bugfix for computing LRT2: LRT2=nan
adds 4efe431 * Updated samtools to the latest * Added seqtk.c * Updated wgsim.c * release samtools-0.1.18
adds df50415 converted padded SAM to unpadded SAM
adds 48a039b added the ace2sam converter
adds 8d24fb5 unpadded output
adds 543a9fc changes from git
adds a9a8e77 bugfix: wrong SP; missing DV in the VCF header
adds 77734b9 Incoporated changes from Nils Homer.
adds 3d8c0bd Two auxilary Lua scripts
adds ddae7dd another example, used by g1k for QA
adds 047fdd5 doc for downsampling
adds 6a5b7e3 Removed SVN ChangeLog; merged my private github Log to ChangeLog.old
adds dc27682 On behalf of Petr: multi-allelic GT
adds 8928103 Initial release of bamcheck and plot-bamcheck
adds 248e7fe Added rule for bamcheck creation
adds 6c564bf Compile cleanly from top-level Makefile. Check for out of bounds tids.
adds 4e0a2f8 updated with the latest bgzf library
adds e50413d preliminary implementation; not tested
adds d46afb5 multi-threading working on toy examples
adds bbf6f36 bugfix in caching
adds 65d1a7c use conditional variable
adds 3f2fa92 avoid wasting CPU time by the master thread
adds bd005db updated the alphanum comparison function
adds 7f4fd36 added mt comression to merge
adds d496e59 added .gitignore
adds 9d415a4 multi-threaded sorting
adds 4c016a8 change the default block size in sorting
adds 64fd9dc sorting also considers strand
adds 27dd510 name sorting checkes READ1 and READ2
adds 8cf3299 bugfix: downsampling not always working
adds 185e80b Merge branch 'master' into mt
adds 17d5671 optionally surpress /[12] in bam2fq
adds d07731e control compression level at command line
adds 81b4ff8 a little more accurate mem estimate
adds 3db228b change SO
adds 3fa88ab move seqtk to a separate project
adds fbb4b13 filter on query sequence length (not aln len)
adds 9970092 Initial release of bamcheck and plot-bamcheck
adds 3248eee Added rule for bamcheck creation
adds 8f9081f Compile cleanly from top-level Makefile. Check for out of bounds tids.
adds 83a7562 Helpful error message on bad CIGAR in unpad_seq
adds 133a2bf Support CIGAR X/= in depad
adds 70c84f4 Check current reference sequence matches RNAME in samtools depad
adds fe8fbc9 Cope with CIGAR D or P to mark gaps in an embedded padded reference
adds 181c7c1 Add TODO note about reference lengths
adds 19657fe Correct my error message; assed some comments
adds bb67db9 Record actual sequence in unpad_seq (fixes apparently harmless bug)
adds f6df8de Include leading CIGAR P operators in 'samtools depad'
adds 2594fb7 Tolerate CIGAR H operators in 'samtools depad'
adds ccbf518 Cope with leading CIGAR H (or H and S) in 'samtools depad'
adds 7327253 Cope with trailing CIGAR H (or S and H) in 'samtools depad'
adds 33657bf Check reference length in BAM header against embedded reference in 'samtools depad'
adds 7e7b219 Merge pull request #2 from peterjc/depad
adds 0ab78dd Merge branch 'master' of github.com:samtools/samtools into mt
adds 0f2614c shrink bam1_t::m_data when sorting
adds 63b27f1 compiling errors on some machines
adds e796ff1 Temporary fix to prevent segfault in kpa_glocal
adds 0fab6af Merge branch 'master' of github.com:samtools/samtools
adds 5941304 Merge remote branch 'main/master'
adds 1dc8e7e Removed glibc dependency (getline)
adds 93d8193 On behalf of Bradford Powell: fixed typo in VCF header, output DV not DP
adds ece9944 Added check for out-of-bounds indels at the end of reads
adds d9c7115 updated to the latest kseq
adds b224b0d change getline() to mygetline()
adds fa6c558 r572: added "bedcov" command
adds 958246a Indexed access can be now combined with target regions. The number of mapped bases more accurate now with -t.
adds c560dce Resolved merge conflict
adds 1ef8ee3 init_regions: check for non-matching sequence names
adds 8c3ff0e Reverted to the previous behaviour, the unmapped reads are not removed. Added -r switch for backward compatibility.
adds 859feef Added -f, -F options. Count and plot indels per cycle for each mate pair separately.
adds 3dbef58 added length threshold
adds 9f851f0 bugfix: bgzf-mt may write prematured output
adds e04c20c added bamshuf from htslib
adds 856d533 change the default clevel to 1 for speed
adds 1250c05 Merge branch 'master' of github.com:samtools/samtools
adds 8c15f91 Fix to prevent long stretches of Ns to be mistaken for indels; Always output the most likely ALT allele
adds 183e4cb The -E switch to recalculate extended BAQ on the fly, ignoring existing BQs
adds eb4c2eb Fixed errors introduced by the 8c15f916dabce475febdf508a9cc0c708c5a7747 commit.
adds 9eb6e63 New -s option for multisample BAMs: include only reads from a given sample in the display
adds 6d9a40f New -p option to start tview at desired position
adds fd2ea98 Update bam1_core_t and bam1_t documentation
adds 9f11826 Fix missing declaration for getopt on Mac OS X
adds af97a7b Merge remote branch 'rq/getopt_mac'
adds fc236a1 Refine logic for removing superfluous P ops (still testing ...)
adds 24d1a2d More elegant solution to avoid superfluous leading P ops
adds d2496f2 Fix silly typo
adds 62254fe Fixed the next silly error on that line.
adds 6b9aa77 Fix buffer overflow in 'samtools depad' with CIGAR D operators
adds ccb7838 Revert one of my earlier changes - Heng was right, CIGAR P not sensible in a padded reference
adds a46b631 Add a tiny bit of help text to 'samtools depad' command.
adds 507c3e9 Adding a usage function to 'samtools depad' following 'samtools view' style
adds 6714aa0 Minimal 'samtools depad' command line parsing (-? only so far)
adds 3d8051c Support SAM or BAM input/output in 'samtools depad' (default still BAM -> BAM)
adds ededaf7 Add reference FASTA file to 'samtools depad' command line (not used yet)
adds dc39f05 Load FAI in 'samtools depad' (not used yet)
adds 685647d Use FASTA file when no embedded reference in 'samtools depad'
adds ed708a6 Check embedded reference against FASTA if given in 'samtools depad'
adds e3bb71f Catch missing reference error in faidx (avoids floating point exception)
adds 8919a74 Wording of error messages
adds 09ad722 SAM/BAM input to 'samtools depad' not linked to FASTA reference
adds 2b4d9b1 Calculate unpadded reference length, update BAM header (SAM header pending)
adds 9b352ed Update @SQ lines during 'samtools depad'
adds 9e24479 Merge pull request #11 from peterjc/depad2
adds f35c82f fixed a couple of minor compiling warnings
adds 0b3418c r579: after merging Peter's depad changes
adds 0b184e9 Merge branch 'master' of github.com:samtools/samtools
adds 50be08b r580: bugfix - bam_aux_get() error given 'f' type
adds 5457893 First attempt at updating MPOS in 'samtools depad'
adds 4f0d8b9 Tweak order free things (avoids an 'samtools depad' seg fault on error)
adds f5c3477 Fix 'samtools depad' seg-fault when MPOS/PNEXT given but MRNM/RNEXT is not
adds 9737475 Merge pull request #14 from peterjc/depad3
adds 12c0954 New --GC-depth option to bamcheck. Take into account not so frequent CIGAR codes. Fix in realloc_buffers. Prevent segfault with long command line options; Set xrange correctly in plot-bamcheck coverage.gp
adds 2e9880c GC-depth calculation now more robust to small GCD bin sizes
adds 700d451 New -p switch for increased sensititivy of indel-calling. Here -m and -F are used per-sample which enables to detect rare indels in low-coverage bams. Experimental.
adds ec294ad Alternative model for multiallelic and rare-variant calling. Proof-of-principle implementation.
adds 74e6aeb Bug fixes
adds faf76ae VCF annotations with and without -m and more robust rm_info
adds ec8ca3b Allow filtering by read group or sample name in bamcheck. Bug fix in rm_info.
adds da45f88 Fix in output of missing haploid genotypes
adds 5cf9f20 Use int64_t to prevent count overflow in view -c; on behalf of Joshua Randall: Set y2range in quals2.png plot
adds bfcd9b3 Fix in insertion cycle calculation of rev reads
adds a71383e Merge remote branch 'remotes/pd3/master'
adds 70c740f Complain when BAM cannot be open. Severe bug fixed in -m haploid calling.
adds 4a1c610 Changed default reflen; more informative error message when GCD bin size too small or reflen too big
adds 72d6457 Drop empty bins from coverage distribution
adds e08e3fa More user-friendly error output
adds 269cdd7 Merge remote branch 'remotes/pd3master/master' into develop
adds 2bc11e5 bamcheck: Fixed a bug introduced by previous change igcd to uint: not a good idea to init with -1.
adds 3f2ddb8 bamcheck: max quality value increased to 255 to handle missing qual field; pairs with IS=0 can still count as paired; output IS=0 stats as well
adds 0449d3d misc/Makefile, on behalf of ghuls: changed the order of bamcheck rules with -lz last
adds 694a8ae bamcheck: New stats, number of pairs mapped to different chromosomes
adds 4b0058f bam_plcmd.c: added sanity check in read_file_list, complain if file list is not a file list
adds c49928a bam_plcmd.c: more descriptive -b usage help message
adds 64275b4 ksort.h: declared __ks_insertsort_##name as static to compile with C99. (On behalf of Hanspeter Niederstrasser.)
adds 43e736c bam2depth: Enabled reading the list of BAMs from a file list
adds 3f45f4a bamcheck: New stats - the number of QC failed reads and non-primary alignments
adds 17abb78 mpileup: New --rf and --ff options for filtering reads
adds 39c526e big fix: using samtools view file.bam gibberish returns alignments; iter not checked against kh_end
adds 7ff3109 fixed missing braces
adds 3a1bd4d Merge branch 'vsbuffalo-master' into develop
adds 0ccd9d3 bamcheck: new stats, number of filtered vs raw sequences
adds 4773f0e dump log-likelihood
adds 3880f18 ...
adds 0e2f13b cont
adds 1bdc079 works with curses
adds 5193fbf cont
adds 307c147 works
adds 1ea6041 cont
adds 9bb4d59 fix html
adds 607d7a0 Merge remote branch 'remotes/pierre/master' into develop
adds e9939ca Adding -f flag to samtools sort to give output name directly.
adds c857677 bcftools view: always output the header, even when no other arguments are given
adds dacaaf5 bcftools view: Exit with an error if the -l file cannot be read
adds 2fa4cde Fix memory leaks: * When downloading a remote FASTA index * When indexing a BAM, we can't open the FAI file * When indexing a BCF, we can't open the index file * Parsing a VCF header with no sample line * Encountering multiple adjacent tabs in a SAM header
adds dbc7644 Merge pull request #30 from leecbaker/master
adds 496174d Merge branch 'master' of github.com:samtools/samtools
adds 3f820f8 Fixed brackets missing in the previous commit
adds 125ac89 backup commit
adds 6842e44 backup commit
adds 60e0a84 Merge remote branch 'remotes/master/master' into fb-annots
adds 17e1513 mpileup: New HWE, QBD, RPS annotations. Modified VDB (beware: this version of VDB may be broken). Fix in indel calling: Ignore insertions with N's. Output contigs in the VCF header. New sam_header2tbl_n() API call.
adds 9a8d2b3 Updated man pages
adds 941fbbb Get rid of %ld-with-int64_t warning on Mac
adds 96b5f22 Merge remote branch 'pd3master/master'
adds 0f47d4e Updated NEWS document
adds 8efed9e Version bump
adds 44428cd bcftools: version bump
adds e7e57af mpileup fix: Print error message and exit when no files given. (On behalf of Gert Hulselmans)
adds fdec840 mpileup indel hotfix: fix in detecting long stretches of N's. The version string can be now overriden, either directly or using git-stamp Makefile rule
adds 4b70907 The indel stats (IS) annotation splitted into two: IDV and IMF
adds 4dde8f5 bgzip now compiles
adds 7c3295b Update BIN values in 'samtools depad'
adds 8e3b3f2 Verify old BIN value of reads during 'samtools index'.
adds efc19a3 Update 'samtools depad' help text regarding FASTA reference file
adds 1278f58 Should update POS on unmapped reads in 'samtools depad'
adds ba21caf Slightly more detailed error message for debugging.
adds 99b55f5 Merge pull request #43 from peterjc/depad_bins
adds be1abba Show reference name in bad BIN error message
adds 698a60f Correct BIN check for CIGAR less reads
adds 28391e5 Merge pull request #44 from peterjc/check_bins
This update added new revisions after undoing existing revisions.
That is to say, some revisions that were in the old version of the
branch are not in the new version. This situation occurs
when a user --force pushes a change and generates a repository
containing something like this:
* -- * -- B -- O -- O -- O (5761c3f)
\
N -- N -- N refs/heads/master (28391e5)
You should already have received notification emails for all of the O
revisions, and so the following emails describe only the N revisions
from the common base, B.
Any revisions marked "omits" are not gone; other references still
refer to them. Any revisions marked "discards" are gone forever.
No new revisions were added by this update.
Summary of changes:
Makefile | 12 +-
bam.h | 6 +-
bam2bcf.c | 2 +-
bam2bcf_indel.c | 2 +-
bam_index.c | 17 +-
bam_plcmd.c | 5 +
bcftools/bcf.h | 6 +-
bcftools/call1.c | 6 +-
bgzip.c | 2 +-
debian/README.Debian | 29 ----
debian/changelog | 180 ----------------------
debian/compat | 1 -
debian/control | 43 ------
debian/copyright | 105 -------------
debian/gbp.conf | 9 --
debian/libbam-dev.install | 6 -
debian/patches/fix_coverage_cap.patch | 14 --
debian/patches/fix_example_makefile.patch | 38 -----
debian/patches/fix_segfault_with_small_ref.patch | 53 -------
debian/patches/series | 3 -
debian/razip.1 | 28 ----
debian/reference | 12 --
debian/rules | 24 ---
debian/samtools.bash-completion | 21 ---
debian/samtools.docs | 2 -
debian/samtools.examples | 6 -
debian/samtools.install | 16 --
debian/samtools.manpages | 2 -
debian/source/format | 1 -
debian/upstream | 19 ---
debian/watch | 2 -
misc/bamcheck.c | 4 +-
padding.c | 71 +++++----
33 files changed, 87 insertions(+), 660 deletions(-)
delete mode 100644 debian/README.Debian
delete mode 100644 debian/changelog
delete mode 100644 debian/compat
delete mode 100644 debian/control
delete mode 100644 debian/copyright
delete mode 100644 debian/gbp.conf
delete mode 100644 debian/libbam-dev.install
delete mode 100644 debian/patches/fix_coverage_cap.patch
delete mode 100644 debian/patches/fix_example_makefile.patch
delete mode 100644 debian/patches/fix_segfault_with_small_ref.patch
delete mode 100644 debian/patches/series
delete mode 100644 debian/razip.1
delete mode 100644 debian/reference
delete mode 100755 debian/rules
delete mode 100644 debian/samtools.bash-completion
delete mode 100644 debian/samtools.docs
delete mode 100644 debian/samtools.examples
delete mode 100644 debian/samtools.install
delete mode 100644 debian/samtools.manpages
delete mode 100644 debian/source/format
delete mode 100644 debian/upstream
delete mode 100644 debian/watch
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