[med-svn] [Git][med-team/samtools][debian/experimental] 732 commits: Handle CIGAR N in samtools depad by treating as CIGAR D.
Michael R. Crusoe (@crusoe)
gitlab at salsa.debian.org
Thu Nov 14 19:14:51 GMT 2024
Michael R. Crusoe pushed to branch debian/experimental at Debian Med / samtools
Commits:
597b83e1 by peterjc at 2014-04-15T11:59:11+01:00
Handle CIGAR N in samtools depad by treating as CIGAR D.
This is not ideal, but is much better than not handling the read at all
(which would happen if the assert didn't abort the command).
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df5b8e7d by peterjc at 2014-04-15T13:49:05+01:00
Add return value to unpad_seq to allow abort on error
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a22f9794 by uzbit at 2014-07-23T17:10:53-07:00
Update bam_tview_curses.c
Large scroll up and down with cap K, J
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c8e1a2bf by Petr Danecek at 2014-08-13T08:48:13+01:00
stats: Compute checksum for names/seqs/quals
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2192dda9 by John Marshall at 2014-08-15T11:36:35+01:00
Merge version number bump from master branch
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e3d4eeeb by Shane McCarthy at 2014-08-17T17:09:23+01:00
fix DPR annotation
* Max alleles got changed in 8030ea3 to 5 instead of 4 to
fix a speparate bug, but 4 left at line 127 in bam2bcf.c
when initialising memory. This leads to bug reported in
#274
* Fix this, but also make `B2B_MAX_ALLELES' a constant to
set this number everywhere it is used (@pd3 please check)
* Parsing of tags was broken. the `--tag' options in the
example in #274 should not have been parsed. Should be
fixed now
* Add test output for all `--tags' options
Fixes #274
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a0254aca by John Marshall at 2014-08-18T16:37:22+01:00
No need to initialise array anyway
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a9d452c1 by Christian Krause at 2014-08-18T20:23:34+02:00
fixes #271
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904f1f56 by Christian Krause at 2014-08-18T20:29:08+02:00
fixes #272
- consistent use of /usr/bin/env perl shebangs
- consistent use of 'use warnings;' in favor of perl -w
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6099d570 by John Marshall at 2014-08-19T11:05:01+01:00
Merge stats checksums
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258b4e60 by James Bonfield at 2014-08-19T11:27:35+01:00
Modified the mpileup tests to have local copies of appropriate
reference sequences. All other tests already had this (but
accidentally escaped in some circumstances).
Added a non-existant REF_PATH= to the tests to prevent it using the
default search path and escaping off to the EBI.
See https://github.com/samtools/samtools/issues/279
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f5288ca2 by John Marshall at 2014-08-20T16:18:27+01:00
Replace bcftools+bcf_filter.sh with new vcf-miniview
Add new vcf-miniview test utility, which reads BCF or VCF and outputs
VCF optionally filtered in the same way that the old bcf_filter.sh did.
The sed -r option used by bcf_filter.sh was not available on OS X, and
an installation of bcftools will not necessarily be available on test
machines, notably when testing via travis.
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d0e4a6c8 by John Marshall at 2014-08-20T16:52:02+01:00
Insulate test case from $GREP_OPTIONS
Prevent e.g. GREP_OPTIONS='--binary-files=without-match' from
subverting the expected output.
Perhaps we ought to add 'unalias egrep' somewhere too...
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9579135d by John Marshall at 2014-08-21T11:12:59+01:00
Update expected output with symbolic "<X>" alleles
Since b14b21933b08ccdf7a777ed4a3529edbb03114e9 mpileup outputs a
symbolic allele rather than a plain "X".
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a7e257d0 by John Marshall at 2014-08-21T15:22:56+01:00
Update QS values in expected output, and don't truncate them
Following the lead of f85ac7d492ddf7fd54e9849733c2d66adf874938
(around the time of which the QS computation changed), we should be
regression testing the full values emitted for QS.
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eeb4b225 by John Marshall at 2014-08-21T17:18:30+01:00
Merge minimal MD5 reference area for mpileup tests
Provide a local reference area via $REF_PATH for mpileup/regression.sh
tests (cf 38eda28b81fd3c176f90a0f03d2645fc891167f0's commit message).
(Note that these MD5 files are truncated versions of their full
sequences; just enough to pass the tests.)
Set REF_PATH to an empty value (but not the empty string, as that
produces the default setting), or in general to point within the test
suite, for tests that exercise it -- currently test.pl and regression.sh.
This makes the test suite self-contained for reference areas, and
in particular prevents travis build testing from trying to access
the EBI reference server. Fixes #279.
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56a4e745 by Charles Plessy at 2014-08-22T07:59:29+09:00
Fixes segfault in mpileup when alignment is outside of the ref.
If a read is aligned outside of the reference (possibly due to
reference mismatch or truncation), samtools mpileup will segfault. It
should instead warn, and continue on. This commit fixes this.
Author: Don Armstrong <don at debian.org>
Date: Thu, 22 Dec 2011 17:42:44 -0800
Debian-Bug: https://bugs.debian.org/653042
Forwarded: https://sourceforge.net/p/samtools/mailman/samtools-help/thread/20111223160030.GC30099@chouca.igloo/
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f62826fe by Petr Danecek at 2014-08-26T09:42:03+01:00
Clean after fix in e3d4eee
- free allocated memory
- strncmp not necessary with hts_readlist
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57e71e72 by Martin Pollard at 2014-08-27T10:56:11+01:00
Fix fixmates for supplementary reads
Currently samtools fixmate will incorrectly perceive supplementary reads as
primaries and consequently mess up the pairing information for the primaries.
This commit fixes this by passing supplementary reads through unmodified.
This also updates flagstat to separate out the statistics for supplementary
and secondary reads.
Signed-off-by: Martin Pollard <mp15 at sanger.ac.uk>
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7b5a9ea8 by Martin O. Pollard at 2014-08-28T16:52:31+01:00
Reduce use of abort, remove assert(fp), pass one string to fprintf not multicall
Reduce use of abort to situations where you might actually want to debug.
Remove assert(fp)'s and replace with proper error messages.
Remove a few instances where fprintf is called multiple times rather than just
passing one string to it.
Signed-off-by: Martin O. Pollard <mp15 at sanger.ac.uk>
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f4b63330 by John Marshall at 2014-09-01T17:17:38+01:00
Merge #! fixes to misc/ scripts
Use "#!/usr/bin/env (perl|python)" throughout, to get the interpreter
from $PATH. Use "use strict; use warnings;" in Perl scripts (this merge
commit also re-adds strict in novo2sam.pl). Fixes #273.
(These small changes are not legally significant for copyright purposes,
so years in the copyright notices have not been updated.)
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faf4dd6c by John Marshall at 2014-09-02T16:16:08+01:00
Formatting fixes for better grinding into HTML
In particular, the removed .RE was incorrectly nested.
Also use fancy >= and arrow characters where available.
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7d678aaa by John Marshall at 2014-09-04T15:09:57+01:00
Recanonicalise test/test.pl whitespace -- USE -b/-w TO DIFF/BLAME
This file had a mixture of 4-space and 8-space tabs, which previously
went unnoticed. Manually re-expand tabs to spaces using the right
number of spaces for each tab.
See notes in fcb8af08a6fd3bfcf195407c4ba5bae528ee326d.
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bc00bde9 by Petr Danecek at 2014-09-05T07:50:54+01:00
mpileup: conform to VCFv4.2 spec, version string should be quoted
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1f8267de by John Marshall at 2014-09-09T10:51:50+01:00
Recanonicalise padding.c whitespace -- USE -b/-w TO DIFF/BLAME
This file had a mixture of 1-tab and 8-space indents which previously
went unnoticed. See notes in fcb8af08a6fd3bfcf195407c4ba5bae528ee326d.
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20817a81 by John Marshall at 2014-09-09T12:22:36+01:00
Merge abort/assert reduction (PR #290)
Also update bam_stat.c and bamshuf.c dependencies accordingly.
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a4ca344c by Martin O. Pollard at 2014-09-09T14:05:40+01:00
Fixmates ct fix
Only add ct if not already present. (Fixes #276)
Make addition of ct a non-default option.
Signed-off-by: Martin O. Pollard <mp15 at sanger.ac.uk>
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f2b42d4c by John Marshall at 2014-09-09T14:45:54+01:00
Merge fixmate ct improvements (PR #292)
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8c908dfa by John Marshall at 2014-09-09T15:12:15+01:00
Remove view -Q qual_scale option
It's unclear what it might be useful for. Closes #154.
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b67461fa by James Bonfield at 2014-09-09T15:43:24+01:00
Free the kstring allocated in bam_fillmd1_core in all cases
Rewrote the logic to avoid unmapped reads bailing out early, negating
the (undocumented) -q and -d options. Fixes #143, closes #293.
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ef00bd86 by John Marshall at 2014-09-11T13:18:57+01:00
Describe compression level settings
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3d6431d1 by Charles Plessy at 2014-09-17T06:47:20+09:00
Merge branch 'debian/experimental' into debian/unstable
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edc09e47 by Charles Plessy at 2014-09-17T06:54:22+09:00
Prevent Makefile from including local copy of the HTSlib.
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932819f0 by Charles Plessy at 2014-09-17T06:58:07+09:00
Build for Unstable.
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8a118f66 by Charles Plessy at 2014-09-17T08:12:12+09:00
Build-depend on libhts-dev...
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7fe38389 by John Marshall at 2014-09-17T15:20:34+01:00
Use hash table to merge reference sequence headers
Merge in each new collection of @SQ headers via a hash table rather than
using an O(n^2) approach. Fixes #260.
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5c49bf94 by James Bonfield at 2014-09-17T18:06:36+01:00
Fixed samtools flagstat to use the samFile (htsFile) API instead of
bamFile. This means it can now work on sam, bam and cram formats
instead of only bam.
Also added a call to the hts_set_opt CRAM_OPT_REQUIRED_FIELDS to
indicate that we do not need to decode other data fields. This only
affects CRAM at present.
NOTE: This hts_set_opt API is subject to change and usage here is
strictly for testing purposes.
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2a40f2ea by James Bonfield at 2014-09-17T18:15:51+01:00
Switch from hts_close to sam_close, for consistency (they're the same
thing underneath).
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6b2c8c94 by Charles Plessy at 2014-09-18T07:34:47+09:00
Current changelog.
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68ca9776 by John Marshall at 2014-09-19T16:51:42+01:00
Release 1.1: bug fixes
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f69f4123 by Andreas Tille at 2014-09-22T12:26:29+02:00
Versioned Build-Depends libhts-dev >= 1.0
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0446ed7c by Charles Plessy at 2014-09-23T09:36:05+09:00
Conforms with Policy 3.5.6.
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8c928df2 by Charles Plessy at 2014-09-23T10:07:01+09:00
samtools (1.0-1) unstable; urgency=low
[ Charles Plessy ]
54ca0c1 Merge with upstream's develop branch.
241a731 razip was removed from samtools.
dc25b81 debian/watch: also track release candidates.
07aaf71 Indicate repository layout in git-buildpackage conf. file.
* debian/control
8bc0fb7 Stop depending on CDBS and quilt.
e613142 Drop static libbam, replaced by the dynamic libhts (Closes: #544976).
b5f284c Build-depend on tabix for the regression tests, that use bgzip.
9febad6 Recommend python since samtools installs a python script in /usr/bin.
0446ed7 Conforms with Policy 3.5.6.
* New package samtools-test
7293cca Create a test package for the test data.
6bd7b89 Adjust install file for two-package build.
caff5f5 Clean before installing test files (this removes compiled files).
* debian/rules
c930cbb Use Debhelper instead of CDBS and rely on the new upstream Makefile.
845581d Adjust for dynamic linking.
d859052 Indicate path to packaged bgzip.
cb23517 Mimick Makefile's CPPFLAGS.
aee1c6c Allow parallel building.
edc09e4 Prevent Makefile from including local copy of the HTSlib.
* debian/patches
f73d764 d062687 Refreshed patches.
2c52f6a 61ac2c5 Forwarded patches on GitHub.
b8eb378 Dropped fix_example_makefile.patch, obsolete.
66079b9 Correct path to python interpreter.
218c1c1 Modify Makefile to facilitate dynamic linking.
[ Andreas Tille ]
f69f412 Versioned Build-Depends libhts-dev >= 1.0
-- Charles Plessy <plessy at debian.org> Tue, 23 Sep 2014 09:36:27 +0900
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c87f8ce9 by Charles Plessy at 2014-09-23T18:31:59+09:00
Add autopkg tests.
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1f661b25 by Charles Plessy at 2014-09-23T18:32:48+09:00
Current changelog.
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db22ee99 by John Marshall at 2014-09-23T17:16:19+01:00
Merge version number bump from master branch
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b7c4b4d0 by John Marshall at 2014-09-24T14:28:12+01:00
Ensure usage tests have a terminal on stdin
Subcommands (starting with samtools stats) given no arguments choose
whether to filter stdin or to display their usage depending on
isatty(STDIN_FILENO). When testing that usage messages are produced,
ensure commands get a terminal on stdin; otherwise skip the tests
if a terminal cannot be arranged. Fixes #300.
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c448d484 by Charles Plessy at 2014-09-25T08:22:09+09:00
Merge tag '1.1' into debian/unstable
Bug fix release
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d12ab1ed by Charles Plessy at 2014-09-25T08:22:21+09:00
Merge branch 'develop' into debian/unstable
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7c50b7b7 by Charles Plessy at 2014-09-25T08:54:27+09:00
Removed python-wrong-path-for-interpreter.patch, solved upstream.
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dcc1da7a by Charles Plessy at 2014-09-25T08:55:37+09:00
Removed sed command redundant with patch dynamic-build.patch.
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91356d65 by Charles Plessy at 2014-09-25T09:05:17+09:00
samtools (1.1-1) unstable; urgency=medium
c448d48 Merge tag '1.1' into debian/unstable
d12ab1e Merge branch 'develop' into debian/unstable to solve issue
with regression tests needing a pseudo-terminal.
See https://github.com/samtools/samtools/issues/300
c87f8ce Add autopkg tests.
7c50b7b Removed python-wrong-path-for-interpreter.patch
(issue solved upstream).
-- Charles Plessy <plessy at debian.org> Thu, 25 Sep 2014 09:04:20 +0900
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281bf0a1 by John Marshall at 2014-09-25T11:52:12+01:00
Recanonicalise regression.sh whitespace -- USE -b/-w TO DIFF/BLAME
This file had mostly 8-space tabs, which previously went unnoticed.
See notes in fcb8af08a6fd3bfcf195407c4ba5bae528ee326d.
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6c2d9cd5 by Charles Plessy at 2014-09-25T21:39:17+09:00
Build-depend and recommend libio-pty-perl for the regression tests.
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d3946de8 by Charles Plessy at 2014-09-25T21:40:28+09:00
Current changelog.
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9c4099fb by John Marshall at 2014-09-29T13:51:26+01:00
Set output file threading only if there is an output file
In particular, there is no output file with -c. Fixes #302.
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6ce5671a by Charles Plessy at 2014-10-01T17:52:37+09:00
Make autopkg test depend on tabix.
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29395a56 by James Bonfield at 2014-10-01T11:36:23+01:00
Fixed a buffer overflow when dealing with cigar strings ending with a
deletion.
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089ecbe7 by James Bonfield at 2014-10-01T12:06:29+01:00
Improved fix to mpileup. The previous one just skipped bases where we
have no quality. This still includes them in the pileup, but with 0
qual instead.
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418fc0c6 by James Bonfield at 2014-10-01T12:10:40+01:00
Also fix buffer overrun on data where the sequence is "*".
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2fac99b5 by James Bonfield at 2014-10-01T12:14:33+01:00
Fixed up test data, now that it correctly outputs "n" instead.
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056ae75d by pd3 at 2014-10-01T13:26:34+02:00
Merge pull request #306 from jkbonfield/mpileup-fix
Mpileup fixes
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59c56f0b by John Marshall at 2014-10-06T11:37:03+01:00
Man page formatting fixes
Use hyphens to introduce options rather than en dashes
(addresses samtools/www.htslib.org#5 for samtools man page).
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5ac61a29 by John Marshall at 2014-10-08T10:33:51+01:00
Write failure messages to stderr
No difference by default, but enables highlighting the failures or
capturing them by redirecting stderr.
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6f1c154d by John Marshall at 2014-10-10T17:03:21+01:00
Maintain HEAP_EMPTY invariant when an input is empty
Ensure h->b is NULL when we hit EOF on the first read, just as it is
when we hit EOF later in the file. Fixes #309 and also prevents a
memory leak for an input file with no records.
Also use bam_init1()/bam_destroy1() instead of creating and destroying
bam1_t structs by hand.
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d2e8d7ac by John Marshall at 2014-10-20T13:04:28+01:00
Avoid using htsFile is_foo bits directly
Use the new public hts_get_format() facilities. Requires htslib
commit 529ca88071e775a488e4108945d5bd863a4190f0 / version 1.2 or later.
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45801506 by Petr Danecek at 2014-10-21T11:28:18+01:00
Reflect changes in htslib API
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01465e80 by Peter Cock at 2014-10-29T16:11:45+00:00
Fix typo in 'samtools flagstats' output
supplimentary --> supplementary
Reported by Daofeng Li on the samtools-help mailing list:
http://sourceforge.net/p/samtools/mailman/message/32983845/
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6c170712 by James Bonfield at 2014-10-30T10:24:16+00:00
Added a test for specifying the reference via samtools -T. This
appeared to work in our previous tests, but did not due to the code
sneakily reverting to the @SQ UR: field instead.
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c02491f0 by John Marshall at 2014-11-03T16:06:29+00:00
Merge origin/develop, prefering avoiding using htsFile internals
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dc1f4389 by Petr Danecek at 2014-11-03T16:15:07+00:00
stats: Calculate mismatches per cycle for unclipped length
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6b249e2c by Petr Danecek at 2014-11-03T16:15:12+00:00
Merge branch 'develop' of github.com:samtools/samtools into develop
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4a2320a4 by John Marshall at 2014-11-03T17:45:04+00:00
Avoid "my" variable redeclaration [minor]
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a25229a9 by John Marshall at 2014-11-04T10:42:47+00:00
Prevent warnings when compiling on a 32-bit host [minor]
Avoid "%zu" as this C99 library functionality is not supported by MSVC.
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c61d8d1e by John Marshall at 2014-11-04T14:49:29+00:00
Merge origin/develop into develop
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63533673 by peterjc at 2014-11-05T12:00:21+00:00
samtools bam2qf option to force FASTA or FASTQ output
This addresses issue #313 - the current behaviour (left as the
default) produces a mixture of FASTQ and FASTA depending on if
each individual read has quality scores or not.
While some tools/parsers will handle mixed files like this, others
will have trouble. This is a problem with systems like Galaxy with
a strict datatype system.
I wanted to use -O for the new output format argument (to follow
the pattern set in samtools sort/rmdup/fixmate) but that is already
taken for the original quality option.
Note that if samtools bam2fq is called forcing FASTQ output, this
currently will use a default PHRED quality score one 1. This value
might make sense to add as a further command line option?
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76300af9 by peterjc at 2014-11-05T16:07:36+00:00
Set default FASTQ quality with samtools bam2fq -v INT
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bca67a95 by John Marshall at 2014-11-12T17:32:15+00:00
Convert bam2bcf_indel.c to use the htslib API directly
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9e3bbcf0 by Martin Pollard at 2014-11-12T17:38:21+00:00
Update comment documentation for bam_mate
Clarify how we now handle supplementary reads and note limitation.
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19c9f67b by John Marshall at 2014-11-18T09:23:55+00:00
Remove unused kaln.c, kaln.h global aligner
The kaln global alignment functions have been unused in
bam_md.c since 51f014165fb63b2b9b86db80ea4681f9351453a1 and
bam2bcf_indel.c since bf8b35cc189c6c846f01752f9e9500a3c08cd9b1.
- - - - -
29b03673 by peterjc at 2014-11-20T09:57:09+00:00
Replace cryptic 'minQLen' with real description
[Modified from Peter's suggestion: as l_qseq == cigar2qlen, we don't
need to mention "mapped length" or "CIGAR".]
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8dd3761a by John Marshall at 2014-11-24T10:13:48+00:00
Use bam_init1/bam_destroy1 instead of creating/destroying by hand
Prefer explicit NULLing to historically non-portable memset obscureness.
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3fdca5b6 by John Marshall at 2014-11-27T10:44:21+00:00
Make samtools merge work with SAM input files
The iterator API doesn't (yet) work with SAM files, as there's no way
to provide the file's headers when initialising or using the iterator.
For SAM files (in the absence of -R REGION), keep the headers around so we
can use sam_read1() rather than sam_itr_queryi(HTS_IDX_REST)/sam_itr_next().
(This will likely be followed up with an option to write SAM output.)
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5d6a1e32 by John Marshall at 2014-12-02T10:27:12+00:00
Avoid crashing on unopenable files [minor]
Akin to fclose(), sam_close() requires the file pointer given to it to
be non-NULL; akin to free(), hts_itr_destroy() does not. Fixes #327.
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7f47a7cc by John Marshall at 2014-12-09T13:48:23+00:00
Parse mpileup -r region against the right file's headers
Restore the code prior to a bug introduced in e7ae7f96c7e78a2dd6eabdaed57037c483951929.
Amongst other things, this ensures that files without the given
reference sequence are reported as failing to parse the region.
Move the setting of data[i]->h lower in the loop to prevent similar
bugs in future. Ensure that data[i]->iter is always explicitly set.
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f3f3d6d7 by John Marshall at 2014-12-11T17:51:23+00:00
Large chromosome test case now passes
Fixed by samtools/htslib at ce1a547f0e01d32fbffb62efbcca51c6ddc77d34.
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c06f698c by Martin Pollard at 2014-12-16T15:47:56+00:00
Add a few comments to pileup and errmod code, move some existing ones to slightly better positions.
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311926c7 by Gianluca Della Vedova at 2015-01-06T16:34:02+01:00
Fix typo.
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f0c42fee by Nathan T. Weeks at 2015-01-09T15:58:42-06:00
Vastly improve performance when many header lines
On at least systems with glibc, regexec() performance suffers greatly
for long search strings. This greatly impacted the runtime of samtools
merge when merging bam files with many (hundreds of thousands or
millions) header lines.
This fix replaces the use of regular expressions in pretty_header() with
string.h functions. Whereas pretty_header() previously could take days
to process over 6 million header lines on systems with affected regular
expression implementations, it can now complete in under a second.
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2bcfffdc by James Bonfield at 2015-01-12T14:23:38+00:00
Added various hts_set_opt calls to set the CRAM_OPT_REQUIRED_FIELDS
and CRAM_OPT_DECODE_MD options to avoid doing unnecessary decoding
work.
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a5138277 by James Bonfield at 2015-01-14T13:56:59+00:00
Merge pull request #299 from jkbonfield/cram3
Cram3 updates
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581e7073 by John Marshall at 2015-01-16T13:02:15+00:00
bamtk.c requires only hts_version(), not <bam.h>
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446aae08 by John Marshall at 2015-01-27T09:01:37+00:00
Happy New Year
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e2ce81d4 by James Bonfield at 2015-01-28T14:17:49+00:00
Added checks to sam_hdr_write() return value.
Samtools view no longer blindly continues when it failed to write the
header. This avoids silent creation of broken CRAM files when the
reference sequences fail to be processed correctly.
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c5df8be2 by Nathan S. Watson-Haigh at 2015-01-30T15:12:40+10:30
Added 'insert size' to the head of the IS section
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0cc7b479 by pd3 at 2015-01-30T08:38:29+01:00
Merge pull request #342 from nathanhaigh/develop
Added 'insert size' to the head of the IS section
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8f503321 by James Bonfield at 2015-01-30T15:26:37+00:00
Documentation: Updated REF_CACHE location details.
The new semantics for default REF_PATH and REF_CACHE are described.
- - - - -
255f97da by John Marshall at 2015-02-02T15:18:41+00:00
Release 1.2: various bug fixes
Also added notes about running against an alternative zlib library.
- - - - -
2e74fb81 by John Marshall at 2015-02-02T16:32:09+00:00
Merge version number bump from master
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f8a62748 by John Marshall at 2015-02-04T13:54:08+00:00
Fix typo -- hat tip @mcshane
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12c4cba0 by James Bonfield at 2015-02-13T09:54:46+00:00
Fixed NM calculation for deletions partially off end of ref.
- - - - -
76870cc4 by John Marshall at 2015-02-19T12:34:05+00:00
Travis builds clone corresponding htslib branch
Rather than always checking out htslib's develop branch, check out a
corresponding branch with the same name if there is one over there.
Default to github.com/samtools/htslib, but allow this to be overridden
e.g. by those who have also forked htslib.
Clone a little faster with --depth=1.
- - - - -
9c6a5c1b by John Marshall at 2015-02-20T11:32:21+00:00
Replace bam_nt16_nt4_table[] by htslib's seq_nt16_int[]
An equivalent was added in samtools/htslib at 9a88137bb6d7e25e82c3cd64a0a54433585a2e4e,
so re-add bam_nt16_nt4_table[] to bam.h in terms of it, undoing the somewhat
misguided 24a52ab78d63e5586f33cc1f57cc2a1e9f2caad7.
Old API code uses bam_nt16_nt4_table[] from bam.h; direct htslib-API code
uses seq_nt16_int[] directly. Nuke all extern declarations.
[NEWS]
* Restored bam_nt16_nt4_table[] to legacy API header bam.h
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f46e5b7b by John Marshall at 2015-02-20T15:06:29+00:00
Implement calmd directly against the htslib API
Remove mode_r and ignore the -S option, as input file formats are
now automatically detected.
- - - - -
78927b70 by John Marshall at 2015-02-20T15:58:55+00:00
Fix calmd -u to write level-0-compressed rather than raw BAM
samtools/htslib at 818a5ed171eb0cc3667a6c01845fca19a17d4478 changed the
meaning of hts_open(fn, "wu") but bam_md.c was not updated accordingly
at the time.
Also added test case. Hat tip @sb10.
[NEWS]
* 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.)
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eb21ebaa by John Marshall at 2015-02-23T15:20:53+00:00
Fix @SQ-LN headers to match actual .fa lengths
As of samtools/htslib at 83190e9076ac8ce0ec51de2688a8845844df2ad3, htslib
fixes up @SQ reference sequence lengths that disagree with the actual
sequences found in the reference.
The reference sequences for these test cases were truncated from the
data they came from; reflect that in the test case data.
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d0c02de3 by John Marshall at 2015-02-23T17:07:29+00:00
Update MD/NM as if by using calmd
As of samtools/htslib at 1f3ef0ae24bca8116b85adb8e584f1e497786687, a trip
through CRAM updates MD/NM tags for reads off the end of a reference
sequence. Update such reads in the test data.
- - - - -
b7ac1e28 by James Bonfield at 2015-02-24T10:14:51+00:00
Added error checking around hts_set_fai_filename() calls.
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356ca470 by John Marshall at 2015-03-05T16:43:28+00:00
Clarify "SAM files differ" error message
Print to stderr for potential highlighting, and also print the
differing lines in question so one can see what the problem is.
- - - - -
918a5676 by John Marshall at 2015-03-06T15:29:32+00:00
For 0.1.x compatibility, "fixmate - -" writes BAM
Pipelines like "... | samtools fixmate - - | ..." worked fine with
samtools 0.1.x but fail ("cannot determine output format") with 1.x.
When no -O option is used, default to BAM as per 0.1.x rather than
failing.
[NEWS]
* "samtools fixmate - -" works in pipelines again; with 1.0 to 1.2,
this failed with "[bam_mating] cannot determine output format"
- - - - -
8a5a91a4 by John Marshall at 2015-03-09T10:26:04+00:00
Writing SAM files may leave htsExactFormat as text_format
[NEWS]
* Fix 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.
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0df98194 by student-t at 2015-03-09T10:41:37+00:00
Update 00README.txt
Fixed spelling.
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a83ac9da by John Marshall at 2015-03-09T11:28:15+00:00
Add sam_index_load() and samfetch() to legacy API
Hat tip @drjsanger.
[NEWS]
* Add 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.)
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7dc40b4f by John Marshall at 2015-03-09T11:37:51+00:00
[tview] Use iterator directly instead of our own sam_fetch() function
- - - - -
e91985a7 by James Bonfield at 2015-03-09T16:20:23+00:00
Merge pull request #361 from samtools/samfetch
Add sam_index_load() and samfetch() to legacy API
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e1714f69 by James Bonfield at 2015-03-11T12:37:14+00:00
Changed from a local misc/md5.c to using the API in htslib.
- - - - -
329c05f6 by James Bonfield at 2015-03-11T12:37:14+00:00
Changes to support the updated htslib md5 interface.
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5dfdf2ed by James Bonfield at 2015-03-11T12:40:39+00:00
Rebased and changed to use updated hts_md5_hex.
- - - - -
d4f5b07e by Shaun Jackman at 2015-03-18T12:07:16+00:00
wgsim: Clarify that -S0 seeds with current time
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ad9d270f by John Marshall at 2015-03-18T14:01:24+00:00
Canonicalise md5sum-lite.c whitespace
- - - - -
b542645c by John Marshall at 2015-03-18T14:57:13+00:00
Merge use of htslib's MD5 API (PR #354)
Requires samtools/htslib at 3accd1934472e2bdd501404f4c1a2e570f868cd1.
Updated remaining hts_md5_hex() call to final version.
- - - - -
dd76533d by Shane McCarthy at 2015-03-19T10:22:40+00:00
samtools dict command to create a sequence dictionary file from a fasta
ala Picard CreateSequenceDictionary
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016c62b0 by John Marshall at 2015-03-19T10:28:26+00:00
[stats] Implement init_regions(), disabled by missing header API
In fact all init_regions() needs to do is look up a tid, for which
an API function is already provided.
[NEWS]
* samtools stats --target-regions option works again
- - - - -
f995b719 by John Marshall at 2015-03-23T16:24:55+00:00
[Makefile] Use user's CPPFLAGS/LIBS variables
Remove INCLUDES and add EXTRA_CPPFLAGS for our own various options that
need to stay set even if the user overrides CPPFLAGS. If we end up with
necessary compiler or linker options or libraries, we'll add EXTRA_CFLAGS,
EXTRA_LDFLAGS, or EXTRA_LIBS accordingly.
Rename LDLIBS to LIBS; it seems that LDLIBS doesn't particularly
exist outside GNU Make's built-in rules. Instead LIBS is configure's
conventional variable for the purpose, so is the right thing to use
for a user-visible variable.
[NEWS]
* 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.
- - - - -
438e92d3 by John Marshall at 2015-03-28T11:03:45+00:00
Merge new dict command (PR #366)
[NEWS]
* new samtools dict command, which creates a sequence dictionary
(as used by Picard) from a FASTA reference file
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9f3da063 by John Marshall at 2015-03-30T13:51:57+01:00
Handle hts_parse_reg() returning NULL
After samtools/htslib at 62e4541d8cbfb4e8250eb42d454e714da9d369d5,
hts_parse_reg() returns NULL when the region could not be parsed.
For an unlikely reference sequence name like "foo:a" this could be a
request for the whole chromosome, so (because we can) handle this case.
Also take advantage of the NULL return to distinguish unknown sequence
names from malformatted regions in error messages. Fixes #353.
For truly ridiculous sequence names like "foo:10-50", users will need
to write whole-chromosome regions as "foo:10-50:1".
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ca446802 by John Marshall at 2015-03-30T15:07:38+01:00
[flagstat] Print "N/A" rather than NaN percentages
Fixes #365. Also improve whitespace around percentages.
Also update bam_stat.o dependencies.
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c94d9378 by Petr Danecek at 2015-04-08T07:31:22+01:00
stats: make cram index work
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84d07029 by Shane McCarthy at 2015-04-13T13:49:35+01:00
copy RG, BC and QT tags to the FASTQ header
bam2fq: pull in option from @lh3 htsbox repo to copy RG, BC and QT tags to the FASTQ header
- - - - -
3f3dbeff by Shane McCarthy at 2015-04-13T13:49:35+01:00
add bam2fq -t option to man page
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33f055c6 by John Marshall at 2015-04-13T15:25:37+01:00
Merge bam2fq RG/BC/QT copying (PR #325)
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428b8e29 by Rob Davies at 2015-04-13T17:25:22+01:00
Make bam_merge_core2 check that sam_index_load() worked.
Add a missing check for a NULL return value from sam_index_load(). This
prevents a segfault when running samtools merge with the -R option on
files that have not been indexed. Instead a message is printed to stderr
and samtools returns a non-zero exit code.
Fixes issue #377.
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23bbfd70 by James Bonfield at 2015-04-14T12:44:57+01:00
Regression.sh fix and mpileup hts_set_fai_filename fix.
Fixed the regression.sh to report failures when a program fails (as
well as succeeds but now gives a different result, which was the
original expectation).
Also fixed the mpileup command causing these regressions. It
previously called hts_set_fai_filename() on NULL filenames.
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738e4026 by James Bonfield at 2015-04-14T12:44:57+01:00
Added -a option to samtools depth.
This produces depth information for all positions rather than just the
ones covered by a sequence. Specifying -a twice will additionally
include depth information on reference sequences not covered by any
read in the file.
Added test cases too, but documentation is (still) absent.
Fixes #374
[NEWS]
* Added -a option to samtools depth to show all locations, including
zero depth sites.
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92899ba6 by James Bonfield at 2015-04-14T13:46:27+01:00
Added missing test output files for samtools depth.
- - - - -
c03c811b by James Bonfield at 2015-04-14T13:48:57+01:00
Swapped bam for sam in samtools depth tests.
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b94f0f2b by James Bonfield at 2015-04-14T14:07:20+01:00
Added "samtools depth" check outputs to testclean target
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f65869ca by James Bonfield at 2015-04-14T16:09:43+01:00
Extra care for floating point comparisons to avoid 32-bit "make check" failures.
Fixes #305
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15f26e82 by Petr Danecek at 2015-04-16T14:05:48+01:00
Resolved merge conflict
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43ca26c4 by Petr Danecek at 2015-04-16T14:07:02+01:00
Reored usage string
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2bf045de by John Marshall at 2015-04-21T16:45:31+01:00
Do min_frac comparisons as double rather than float
This suffices to make x87 also produce the expected results for
humanely-readable min_frac values such as 0.6. Fixes #305.
- - - - -
ff95462d by Joshua Randall at 2015-04-27T10:05:55+01:00
Adds missing sections to samtools man page
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c404615a by James Bonfield at 2015-05-01T17:13:45+01:00
Added --output-fmt-option and --input-fmt-option to merge, sort and view.
Also where absent added --output-fmt and -O too. These allow control
of the CRAM files being generated. For example to sort a BAM file into
a CRAM file (previously not possible), specifying version 3.0 using an
embedded reference, we would use:
./samtools sort -@ 8 --output-fmt cram -T /tmp/_ \
--output-fmt-option version=3.0 \
--output-fmt-option embed_ref \
-o /tmp/foo.cram /tmp/foo.bam
- - - - -
317e6c91 by James Bonfield at 2015-05-01T17:49:10+01:00
Added --input-fmt-options arg.
- - - - -
0736a655 by John Marshall at 2015-05-06T14:04:42+01:00
Merge pretty_header() performance improvement (PR #337)
Renamed copy_records()/et al to copy_headers(), as in this code "record"
usually means a bam1_t rather than a header. Simplified the any-other-
headers loop to iterate over lines directly. Fixes #373 too.
[NEWS]
* Merging files with millions of headers now completes in a reasonable
amount of time (#337, #373; thanks to Nathan Weeks)
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5c3b7271 by John Marshall at 2015-05-06T14:24:02+01:00
Merge x87 floating point precision workaround
Ensure that indel calculations work the same way on x87 as on various
64-bit IEEE platform. Fixes #305; we tried several fixes, as reflected
in this multi-way merge. FLT_EPSILON version preserved for posterity,
and in case we need to revisit this.
- - - - -
7b5c26c8 by Shane McCarthy at 2015-05-07T14:58:45+01:00
allow samtools merge with one input file
* allow samtools merge with one input file
* slight update to usage docs to reflect this
* test that runs merge with one input file
* fix minor bug when using `-r' option to setting RGID from filename -
now strips `.bam', `.cram' and `.sam' extensions.
- - - - -
3023e2c5 by Sendu Bala at 2015-05-12T11:56:37+01:00
added pipe input support to plot-bamstats: use "-" as the bamcheck filename
- - - - -
75ba5410 by John Marshall at 2015-05-12T14:18:27+01:00
Add samtools 1.0 faidx RAZF->BGZF note
This should have been mentioned at the time...
- - - - -
e8f27a32 by John Marshall at 2015-05-12T14:18:27+01:00
Merge @CO headers
In trans_tbl_init(), copy @CO headers to the destination. Possibly
unknown non-standard headers (if any) should just be copied similarly.
The output file still gets an @HD header from the first input file only.
Update test cases correspondingly. See also #390.
- - - - -
1f577c41 by James Bonfield at 2015-05-14T12:28:11+01:00
Rationalised the long option handling for "global" options.
There is a new hts_open_opts too that takes an option structure. This
is a change in behaviour as the former code used hts_open followed by
an hts_opt_apply call to apply the options to the file handle.
Many more sub-commands to-do still. This is largely a patch for the
option infrastructure and a few subcommands to test it with.
- - - - -
a515c2ce by James Bonfield at 2015-05-14T15:25:22+01:00
Changed bamshuf to use sam_open instead of bgzf_open so it can handle all formats.
- - - - -
30220210 by James Bonfield at 2015-05-15T11:28:46+01:00
More --output-fmt-options: fixmate and bamshuf.
- - - - -
14e9a5ec by James Bonfield at 2015-05-15T14:42:53+01:00
Fixed bam split test harness.
- - - - -
942d55f8 by James Bonfield at 2015-05-15T15:55:48+01:00
Updated to keep in sync with htslib changes (hts_open_format et al).
- - - - -
ff29be9a by James Bonfield at 2015-05-15T17:37:44+01:00
Fixed bamshuf to use BAM level 1 for temp files and .%s for final output file.
- - - - -
dd779efd by James Bonfield at 2015-05-15T17:56:31+01:00
Fixed use of hts_opt_add following change to htsFormat struct.
- - - - -
4e2cdee2 by James Bonfield at 2015-05-15T17:57:01+01:00
Added --input-fmt-option to bam2depth.
Also fixed report of errors.
- - - - -
b0525f3e by James Bonfield at 2015-05-18T09:41:46+01:00
Added pointer to our own published zlib benchmarks.
- - - - -
367d754f by James Bonfield at 2015-05-18T14:49:08+01:00
More sub-commands with --input-fmt-option.
This provides a way of specifying references to CRAM where the command
doesn't accept a reference and to specify the number of decoding threads.
- - - - -
723ee29f by James Bonfield at 2015-05-19T16:36:56+01:00
Fixed bedcov usage. (I'm impressed the test harness spotted this!)
- - - - -
52094e19 by James Bonfield at 2015-05-19T17:38:28+01:00
Improved usage of CRAM_OPT_REQUIRED_FIELDS.
- - - - -
aa7eb08e by James Bonfield at 2015-05-20T09:48:33+01:00
bam2fq: fixed -O with CRAMs. Also now detects decoding error (BAM or CRAM).
- - - - -
b9af7eb9 by James Bonfield at 2015-05-20T17:05:51+01:00
More long option handling.
Removed the --verbose global option (it was only there as a test for
options with no argument).
Added --reference option which applies it to both input and output
format.
Updated a few commands from the older sam_open / hts_opt_apply syntax
to sam_open_format instead.
Added more error checking to marge, sort and split.
Samtools split and bamshuf now use .bam as the default extension again
when no format is specified.
Samtools cut_target now handles both sam and cram format too.
- - - - -
ae2332da by James Bonfield at 2015-05-20T17:48:57+01:00
Fixed an issue causing mpileup --rf and stats --help to fail.
This was caused by the new long options and assign_short_opts only
modifying the first fields rather than expliitly looking for the new
options by name.
- - - - -
af658fbb by James Bonfield at 2015-05-21T09:30:44+01:00
Fixed missing return value in cleanup_state.
- - - - -
55c852fc by Martin O. Pollard at 2015-05-21T16:16:30+01:00
Filename to RG ID header fix when merging, fix tab for space in merge tests
Fixes the fact that the -r option for samtools merge did not add entries to
the header.
Fixes the merge tests where a space accidentally crept in place of a tab in
test_input_1_b.
- - - - -
0e19c9e6 by John Marshall at 2015-05-26T13:15:34+01:00
Change --outfile to --output; document faidx warning
Change dict --outfile to --output, as per the recommended long options
in the GNU Coding Standards.
Document the new faidx duplicate FASTA sequence warning (#380).
- - - - -
c2b423c6 by Martin O. Pollard at 2015-05-26T13:17:33+01:00
Reduce sam view usage fprintf calls
Create a multi-line string rather than calling fprintf dozens of times.
- - - - -
99f2a2c4 by John Marshall at 2015-05-26T13:47:48+01:00
Further tweak samtools view usage display
Don't waste columns on indenting past "Options:".
Use C string pasting for the multi-line Notes string too.
- - - - -
7b346933 by John Marshall at 2015-05-26T13:56:51+01:00
Merge sam view usage code tweaks (PR #396)
- - - - -
62d77118 by Joshua Randall at 2015-05-26T14:08:13+01:00
Adds 'N' and 'Other' columns to `samtools stats` GCC output.
Fixes 376
- - - - -
5e6d7bdb by John Marshall at 2015-05-26T15:22:26+01:00
Update test data for htslib bin corrections
Update test_input_1_a.bam and [23].merge.expected.bam to have the
corrected bin values as per samtools/htslib#208.
Introduce a new test using "samtools index" to regenerate
test_input_1_a.bam.bai. This ensures that the .bai is newer than
the .bam; previously any commit that updated the .bam but not the .bai
(of which this would have been the first) would lead to test failures
due to "The index file is older than the data file" warnings.
Remove unused test_input_1_[bc].bam.bai indices.
- - - - -
57320c5f by John Marshall at 2015-05-27T09:21:33+01:00
Ignore "samtools depth" check outputs
(See also b94f0f2bc9c9b0e04c8a85b8673057a633d1b8df.)
- - - - -
8b8ed6ae by John Marshall at 2015-05-27T11:52:11+01:00
Merge 'N' and 'Other' stats columns (PR #397)
Modified to use a switch (jump table) rather than repeated if-stmts.
[NEWS]
* samtools stats now outputs separate "N" and "other" columns in the
ACGT content per cycle section (#376)
- - - - -
c18f0f59 by Petr Danecek at 2015-05-28T16:29:50+01:00
plot-bamstats: Remove hard-wired 60 columns fasta lines assumption
`plot-bamstats` with the `-r` option had a 60 columns assumption
about the fasta file which made for some strange looking lines
when run with GRCh38 for instance.
- - - - -
23d901ec by John Marshall at 2015-05-29T09:59:53+01:00
Allow "cmd | samtools view" and write usage to stdout
Given just "samtools view", display the usage or view stdin (as per
"samtools view -") depending on whether the input is a terminal
similarly to other subcommands. This makes samtools view act more
like a typical Unix filter in pipelines. Hat tip @jwhsanger.
When it's not an error message (as in "samtools --help view" or just
"samtools view"), display the usage on stdout and exit successfully.
- - - - -
42098f01 by John Marshall at 2015-06-01T11:30:43+01:00
[man page] reorder as per incoming patch [minor]
- - - - -
1fe4b3c8 by John Marshall at 2015-06-01T16:58:59+01:00
Merge man page additions (PR #381)
- - - - -
7802db38 by James Bonfield at 2015-06-02T14:08:12+01:00
Samtools depad fixes (part 1).
Updated the bam header API to use htslib.
Fixed the test data for r051 so that it has the correctly depadded
cigar string.
Fixed the code such that it can now generate the correct output for
r051 too.
Changed the tests from expected fail to expected pass.
- - - - -
9c2461ea by James Bonfield at 2015-06-02T17:34:41+01:00
Switched to using htslib instead of bam.h. Plus CRAM support.
Also had to fix the test data to not have unmapped reads with a CIGAR
string as this isn't supported in CRAM. The change to stop this
blowing up in CRAM now also means that these strings do not get edited
in SAM or BAM either. I think that is valid though as they are
currently nonsensical.
- - - - -
44e1a749 by John Marshall at 2015-06-03T11:35:26+01:00
Merge filename to RG-ID merge fixes (PR #394)
Hand-merged binary test data bin field fixes (cf 5e6d7bdbfbbc12d32328614fba99560895b161a4).
Dropped unrelated -s VALUE usage documentation complexification.
- - - - -
f85deba9 by James Bonfield at 2015-06-03T14:38:22+01:00
Fixes #201 - thanks Peter.
Merge complicated by the ancestry and that this all predates the grand
white-space unification. Joy!
Conflicts:
padding.c
- - - - -
a03575bf by James Bonfield at 2015-06-03T15:21:08+01:00
Merge branch 'develop' into depad
- - - - -
e8044911 by James Bonfield at 2015-06-03T16:55:10+01:00
Added depad documentation.
- - - - -
63c060d8 by James Bonfield at 2015-06-03T17:55:24+01:00
Further CRAM fixes.
CRAM output is now forced to using non-reference mode as clearly we
don't have a copy of depadded reference to compare against.
Also implemented the "TODO" comment. We now have proper @SQ parsing
and fixing.
- - - - -
8a0914e5 by Rob Davies at 2015-06-10T16:08:30+01:00
Add checks for bam_hdr_read and sam_hdr_read returning NULL.
Also bam_header_read and sam_header_read which wrap the _hdr_read versions.
In main_bam2fq(), delay opening the singleton file until after sam_hdr_read
and bam_init1 have completed. This means it won't create an empty file
if either of them fail.
- - - - -
93c45cc2 by James Bonfield at 2015-06-12T14:51:23+01:00
Fixed #79
The reference is fetched during mpileup fetching/callback rather than
once processing a position, as the latter is too late to get the
correct ref seq for performing BAQ realignment.
- - - - -
82002e68 by James Bonfield at 2015-06-12T15:37:47+01:00
Fixed tests.
The tests were superficially manually checked to validate that the
differences are reasonable, but it's not feasible to accurately
calculate the impact of adding BAQ. ce#large_seq.bam now uses -B to
prevent excessive memory usage in realignment.
Also removed some commented out debugging.
- - - - -
5363823f by John Marshall at 2015-06-15T10:26:09+01:00
Avoid using asprintf(), which isn't even a POSIX function
- - - - -
a5f28a0f by Charles Plessy at 2015-06-15T21:23:53+09:00
Merge tag '1.2' into debian/unstable
Bug fix release
- - - - -
71af052b by Charles Plessy at 2015-06-15T21:31:44+09:00
New upstream release ; no new copyright notice nor license term.
- - - - -
712a2160 by Charles Plessy at 2015-06-15T21:43:54+09:00
Corrected syntax.
- - - - -
23e44a41 by Charles Plessy at 2015-06-15T21:44:28+09:00
Removed fix_coverage_cap.patch, obsoleted by -d option.
See https://github.com/samtools/samtools/issues/284
- - - - -
1091aab0 by Charles Plessy at 2015-06-15T21:48:58+09:00
Refreshed fuzzy patches.
- - - - -
c542e84f by Charles Plessy at 2015-06-15T21:59:57+09:00
Build-depend on libhts-dev 1.2.
- - - - -
c789e054 by Charles Plessy at 2015-06-15T22:03:26+09:00
Current changelog.
- - - - -
d2e84d56 by Charles Plessy at 2015-06-16T05:30:09+09:00
Revert last commit, that included patched files by mistake.
This reverts commit c789e05419a795fa01a162aa84419f856d5385b8.
- - - - -
affb220a by Charles Plessy at 2015-06-16T05:30:38+09:00
Current changelog.
- - - - -
e4c31091 by Charles Plessy at 2015-06-16T06:58:56+09:00
samtools (1.2-1) unstable; urgency=medium
a5f28a0 Merge tag '1.2' into debian/unstable
c542e84 Build-depend on libhts-dev 1.2.
6c2d9cd Build-depend and recommend libio-pty-perl.
(Needed for the regression tests.)
23e44a4 Removed fix_coverage_cap.patch, obsoleted by -d option.
1091aab Refreshed fuzzy patches.
-- Charles Plessy <plessy at debian.org> Tue, 16 Jun 2015 06:12:12 +0900
- - - - -
9bbc79ec by John Marshall at 2015-06-16T12:18:38+01:00
Report bam_index_build() errors via stderr and exit status
If bam_index_build() fails, print an error message and fail.
Finally completes fixes samtools/htslib#189, and fixes #362.
- - - - -
a717b052 by James Bonfield at 2015-06-17T10:34:39+01:00
Merge branch 'mpileup-segfault' of https://github.com/Debian/samtools into mpileup_BAQ
jkb: most of the changes in this pull request have been obsoleted by
the restructuring, but the core check still works. Thanks.
Conflicts:
bam_plcmd.c
- - - - -
3b266baa by James Bonfield at 2015-06-17T11:41:50+01:00
Rewrite samtools reheader in terms of htslib API (instead of bam.h).
- - - - -
29d6b58c by John Marshall at 2015-06-18T10:34:52+01:00
Merge depad improvements and conversion to htslib API (PR #404)
Update makefile dependencies and padding.c copyright years.
[NEWS]
* Samtools depad command now handles CIGAR N operators and accepts
CRAM files (#201, #404)
- - - - -
39a35af0 by John Marshall at 2015-06-18T12:04:38+01:00
Merge mpileup BAQ fixes (PR #407)
[NEWS]
* Samtools mpileup 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; #79, #125, #286, #407)
- - - - -
160351ca by James Bonfield at 2015-06-23T15:22:58+01:00
Updated samtools reheader to work on CRAM.
There are now 3 modes:
1) BAM to stdout
2) CRAM to stdout
3) CRAM insitu.
Internally the insitu version is coded with a separate v2.1 and v3.0
CRAM implementation.
Also added tests for the above 3 cases (but not including the soon to
be outdated v2.1 support).
- - - - -
1500934c by James Bonfield at 2015-06-24T17:06:18+01:00
Updates based on pull request comments.
Insitu replace by in-place (and -I vs -i).
SAMTOOLS_VERSION replaced by samtools_version().
CRAM data struct manipulations replaced by an more officially
sanctioned external API in the new htslib/cram.h file.
Note: I haven't manually re-checked version 2.1 files yet. This
cannot be done via the test harness as it depends on the
output-fmt-option branch. I'll do this in a new PR.
- - - - -
a4093290 by John Marshall at 2015-06-25T15:08:54+01:00
Check ref sequence length before examining ref base
Prevent fillmd (and other commands) seg faults due to reads with POS
invalidly beyond the end of RNAME. Hat tip @vvi.
[NEWS]
* 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.)
- - - - -
eca63aa1 by John Marshall at 2015-06-26T09:24:45+01:00
Without regions, default to 1..INT_MAX rather than 1..2^29
Fixes part 2 of #241 for depth and mpileup commands with no region
specified.
- - - - -
66a96860 by Martin O. Pollard at 2015-06-26T15:49:45+01:00
Revise stats to handle SECONDARY and SUPPLEMENTARY flagged reads properly
Break stats main down into smaller functions for readability.
Adjust stats to properly take into account secondary and supplementary reads
by adding code which turns on and off tests based on secondary and supplementary flags.
Add tests with supplementary reads.
Moved collect_original_stats code into it's own function based on feedback from pd3.
Signed-off-by: Martin O. Pollard <mp15 at sanger.ac.uk>
- - - - -
26ddf378 by John Marshall at 2015-07-01T14:27:52+01:00
Merge stats supplementary/secondary fixes (PR #357; fixes #352)
- - - - -
9f0a46f9 by Christopher Smowton at 2015-07-01T16:41:53+01:00
Amend SAM header merge strategy to avoid two quadratic-cost operations and switch from expensive regexes to simple string.h operations.
- - - - -
a1814030 by Christopher Smowton at 2015-07-01T16:44:08+01:00
Merge branch 'develop' of https://github.com/samtools/samtools into header_merge_efficiency
- - - - -
f8454046 by James Bonfield at 2015-07-02T11:41:10+01:00
Use vcf-miniview to bugfix the broken mpileup BCF test.
We don't use -f as it's good to have one test that checks everything
(and fix it if we knowingly break the test).
Fixes #410
- - - - -
cd323165 by John Marshall at 2015-07-06T11:43:48+01:00
Remove unused warning, update copyright years [minor]
Both are detritus from merge 26ddf378770049c02ab0bf2f04a97969c819d40d.
- - - - -
ddcde253 by Heng Li at 2015-07-07T02:17:42+01:00
allow to set the fraction of ambiguous bases
[Fixed typos.]
- - - - -
86b0b1e5 by Heng Li at 2015-07-07T02:17:42+01:00
bugfix: missing inserted allele in output
- - - - -
9ab43798 by Heng Li at 2015-07-07T02:17:42+01:00
output contiguous deletion
- - - - -
c19acd80 by James Bonfield at 2015-07-08T12:44:15+01:00
Fixes #320 - fixed bug in bam_prob_realn_core with QUAL "*".
Also had to change the test files as the expected output has changed
(it's now sane).
- - - - -
41044e36 by Peter Cock at 2015-07-08T14:43:41+01:00
Describe output format in samtools depth usage string
- - - - -
66b2f540 by James Bonfield at 2015-07-08T14:49:35+01:00
Added synonym of -d max_depth to samtools depth for compatibility with
mpileup.
This also (sort of) fixes #322.
- - - - -
d8fab7ac by James Bonfield at 2015-07-08T14:56:34+01:00
Merge branch 'depth_usage' of https://github.com/peterjc/samtools into develop
- - - - -
d968d421 by James Bonfield at 2015-07-08T14:57:11+01:00
Merge pull request #426 from peterjc/depth_usage
Describe output format in samtools depth usage string
- - - - -
6f8478a7 by James Bonfield at 2015-07-08T15:01:51+01:00
Merge branch 'develop' of https://github.com/samtools/samtools into develop
- - - - -
877434b0 by James Bonfield at 2015-07-08T15:06:15+01:00
Fixed accidental white space variation.
- - - - -
d9ff716b by James Bonfield at 2015-07-08T16:48:26+01:00
Fixes #328
Whee, 7 months on and I'm assigned my own bug report. :-)
Samtools sort now returns non-zero exit status when it detects an
error, rather than message received, understood, and ignored!
- - - - -
e72b2455 by James Bonfield at 2015-07-09T17:38:08+01:00
Fixed wgsim bugs.
Insertions on the reverse strand were being added by reverse
direction, so the sequence differed.
Insertions on the reverse strand were being added one base too early.
- - - - -
8f60492d by John Marshall at 2015-07-10T18:03:20+12:00
Reactivate "samtools index bam bam.bai" command
Use sam_index_build2() added in samtools/htslib at e9b7db4474ee82fc33c883cc906985ec56b32802
to implement the 0.1.x two-filename index command. Fixes #199 and the
non-pass-through part of #427.
[NEWS]
* Samtools index's optional index output path argument works again (#199)
- - - - -
e2bb18fe by Sam Nicholls at 2015-07-17T16:48:40+01:00
Add support for multiple file comparison in tests.
* Add `out_map` hash to test_cmd args hash. Keys are the names of
expected output files which map to the path of the expected output
of that particular output.
* Add `hskip` to test_cmd args hash. An integer used to splice out
the desired number of lines from the head when reading the actual
output file in to the `$out` array, allowing for a match to `$exp`.
* `out_map` does not override or intefere with the `out` argument and
can also be used alongside it to check both stdout and multiple
expected output files.
- - - - -
7584cf6f by Sam Nicholls at 2015-07-20T11:25:10+01:00
Allow splitting of statistics on tags
* Removed several 'global' statistics parameters such as
`cov_[min|max|step]`, `gcd_bin_size` to a new struct: `stats_info_t`.
* Each `stats_t` holds pointer to `stats_info_t` to avoid passing the
info structure around to every function that needs access to the
user specified "global" options.
* `output_stats` accepts new first parameter for target FILE*.
* New `init_structures` function accepts a `stats_t` and initialises it.
* `split_hash` khash structure maps RG IDs to an address in memory
corresponding to a `stats_t` for that particular read group.
* New `split_stats` accepts a `stats_t` and `split_hash` and creates a
new `stats_t`, inserting its address in to the hash.
* `all_stats` maintains old behaviour and is written to stdout.
* Other `stats_t` are written to files in the format <bam_fname>_<RG ID>.bamstat
- - - - -
09cf53cb by Sam Nicholls at 2015-07-21T10:30:38+01:00
Use stats_t* over intptr_t in hash
- - - - -
227c142c by Martin O. Pollard at 2015-07-28T16:21:22+01:00
Fix for -c and -p in merge and sort
-Add fix so that -c and -p put the first @RG or @PG into the output
-Add testcase to check the -c and -p
- - - - -
ad1c71e2 by John Marshall at 2015-07-29T10:39:05+01:00
Avoid filenames containing colons, which are invalid on Windows
Windows dislikes <>:"/\|?* in filenames, and colons interact somewhat
oddly with Mac OS X's Finder (which displays them as slashes).
- - - - -
784b4f53 by peterjc at 2015-07-29T11:48:50+01:00
samtools depth usage typo and longer line wrapping
Fixes my typo (repeated 'the') and makes the usage text line wrapping
use longer lines.
- - - - -
598f4a0f by John Marshall at 2015-07-29T13:20:43+01:00
Replace xz-compressed test data file with gzipped equivalent
Avoid xz, which may not be installed by default especially on OS X
or Windows. To improve gzip compression of this data, we only gzip the
interesting fields and reconstruct chromosome/position in fields 1 and 2,
reducing the gzipped data from 3M to 582K -- hat tip @jkbonfield.
(The doubled \\ escapes the backslash from sh(1)'s read builtin.)
- - - - -
04ca9436 by Martin O. Pollard at 2015-07-29T16:09:12+01:00
Enable travis OS X to test cross platform bugs
-Enable travis "osx" platform
- - - - -
09095862 by John Marshall at 2015-07-31T15:16:59+01:00
Merge reheader support for CRAM files (PR #412)
Updated bam_reheader.o dependencies, added *.tmp.* temporary test file
cleaning and renamed new tmp test files, completed s/in situ/in-place/g.
- - - - -
6d6208ad by James Bonfield at 2015-07-31T15:36:01+01:00
Fixed the mpileup test to avoid floating point 32/64 bit issues.
It's a hack as we chop off the last digit rather than rounding
correctly, but it happens to be sufficient for the test data we
currently have. If we later get data that rounds from say 0.9 to 1.0
then we can rewrite it with a bit more cleverness.
Fixes #445
- - - - -
a63070c0 by James Bonfield at 2015-07-31T15:38:35+01:00
Added input/output-fmt-option to man page.
[Moved added section to before REFERENCE SEQUENCES; fixed typos and
improved formatting -- JM.]
- - - - -
75ae6d4d by James Bonfield at 2015-07-31T15:40:36+01:00
Merge branch 'develop' of github.com:samtools/samtools into develop
- - - - -
26f57e3a by John Marshall at 2015-08-03T10:44:37+01:00
Use POSIX awk gsub() rather than GNU gensub()
For example, some Travis build hosts don't have GNU Awk.
- - - - -
1278126d by John Marshall at 2015-08-03T13:31:55+01:00
Preserve TAB characters in command to be executed
Current dash (and apparently whatever bash version travis-osx uses)
read -r translates \t etc escapes into control characters. Ensure
that these survive intact rather than evaporating into spaces: for
uses like "awk -v OFS='<tab>'" the difference is crucial.
- - - - -
1669c256 by John Marshall at 2015-08-03T13:46:35+01:00
Merge FP last digit removal filter (#445)
- - - - -
5812c9b6 by Martin O. Pollard at 2015-08-04T10:43:46+01:00
Add facility to escape regex inputs
Add regex_escape to escape extended regex meta chars.
Add regex_escape calls to ID fields embedded into regex searches.
Add testcase to demonstrate that this fixes #434 and fixes #409.
- - - - -
999def39 by John Marshall at 2015-08-04T12:09:37+01:00
Properly preserve \t and other escape sequences
The problem apparently down to dash's read -r was in fact caused by its
echo builtin translating \t etc. Echo is not portable w.r.t. whether
it parses backslash-escapes or not; fix this properly by using printf(1)
instead.
- - - - -
b8ff342f by Martin Pollard at 2015-08-04T13:32:33+01:00
Misc code cleanups
Replace != with < in for loops in errmod.
Replace 0's with NULL in bam_plcmd.c
Replace exit(1)'s with exit(EXIT_FAILURE)'s in bam_plcmd.c.
- - - - -
d1d3cd2d by John Marshall at 2015-08-05T09:17:34+01:00
Minor sam_opts updates
Constify several parameters, avoid arbitrary length limit in "reference=%s"
construction, change include guard to match filename.
- - - - -
78c23438 by Shane McCarthy at 2015-08-05T14:47:12+01:00
mpileup output updates for VCF4.3
* the unseen allele is to be specified as <*> rather then X or <X>
as has been the case in mpileup for a while.
See samtools/hts-specs at 4a917457cb9be262bbe22634a90ece2e0dd08f48
Note that bcftools call supports X, <X> and <*>,
see samtools/bcftools at 802ff309822b8648cc3b7022e3a72e3312e03279
* add options to output AD,ADF,ADR (samtools/hts-specs#78)
* deprecate DV,DP4,DPR annotations as largely superseded by
the new AD tags
- - - - -
4bf18861 by Shane McCarthy at 2015-08-05T15:11:19+01:00
resolve merge conflict
- - - - -
c03fec6c by John Marshall at 2015-08-06T11:32:26+01:00
Replace assign_short_opts() so struct options can be const
Use the new SAM_OPT_GLOBAL_OPTIONS() to const-initialise the various
struct option lists correctly, so we don't need assign_short_opts()
any more.
For subcommands which have their own additional long options,
assign_short_opts() left incorrect entries behind as it did not shift
all entries when disabling options. Instead we mark disabled options
with '?', so that they are parsed and return '?' from getopt_long(),
signalling a usage display. (It remains to verify that all subcommands
treat '?' appropriately.)
- - - - -
32fd3af9 by John Marshall at 2015-08-06T15:14:03+01:00
Actually test multithreaded Big SAM -> CRAM
(Aaaaaaargh!)
- - - - -
9951654e by Rob Davies at 2015-08-07T17:40:11+01:00
Merge pull request samtools#436 into branch for samtools#419
Also fixed tabs that came in with samtools#419.
Conflicts:
bam_sort.c
- - - - -
4dda6177 by Rob Davies at 2015-08-10T12:09:03+01:00
Make test_trans_tbl_init build and run successfully.
Pass target names hash to trans_tbl_init().
Update setup_test_* functions to initialise the hash with the pre-existing
target names.
Add some printfs to make it easier to find out which tests passed/failed.
- - - - -
71e1a62d by John Marshall at 2015-08-10T15:52:43+01:00
Finish cut_target.c conversion to htslib API
- - - - -
f78373cb by Sam Nicholls at 2015-08-10T23:59:44+02:00
`samtools sort` usage [Fixes #418,#356,#349,#295]
* Removes checking for modern or legacy usage and assumes all usage
follows modern syntax.
* `-T` is no longer required and is set to <in.bam>.tmp.NNNN.bam by default.
* Without `-O`, output format inferred from input with sam_open_mode. For
stdin, bam output is assumed unless specified.
* Updates samtools.1 and bam_sort.c usage syntax.
- - - - -
998188a6 by Joshua Randall at 2015-08-11T10:14:39+01:00
Adds `samtools quickcheck` subcommand
`samtools quickcheck` opens a set of SAM/BAM/CRAM files and
checks that the header of each contains at least one target
sequence, then (currently for BAM files only due to htslib
API limitations) seeks to the end of the file to check
whether the EOF block is intact.
Exits with a zero status if all input files checked out ok,
or a non-zero status otherwise. Can be made to give a list
of failing files (on stdout) using the `-v` option or to be
more verbose (on stderr) by giving additional `v` options.
- - - - -
b1a58545 by John Marshall at 2015-08-13T16:43:36+01:00
Merge --output-fmt-option etc global option handling (PR #395)
Consistently constify bam_tview*.c's *_tv_init() fmt parameters.
Similarly in bam_split.c and bam_sort.c.
Change bam_split.c's %f to %. (similar to the existing punctuation-based
expansions and to other similar tools), and document the added % expansion.
Restore bam_sort.c's bam_merge_core() and bam_sort_core(), which are
potentially used by legacy third-party code.
Add $(sam_opts_h) dependencies, and fix miscellaneous dependencies.
Call sam_global_opt_help() in bam_plcmd.c, bam_tview.c, and cut_target.c.
Fix bedcov.c and sam_view.c usage displays. Fix bam_plcmd.c, bam_stat.c,
and sam_view.c option error handling.
Fix bam2depth.c usage message typos (hat tip @velcrospud).
Correct sam_opts.c whitespace.
- - - - -
8853bc6b by John Marshall at 2015-08-13T16:55:39+01:00
Fix FILE* destination for usage output
- - - - -
b3fb0f29 by John Marshall at 2015-08-13T17:11:43+01:00
Improve man page table formatting [minor]
- - - - -
f246dbc6 by John Marshall at 2015-08-14T09:22:38+01:00
Fix stats.c memset() thinko
Fixes segfault whenever realloc_buffers() is called. Hat tip @vvi.
- - - - -
f282777b by John Marshall at 2015-08-14T12:52:55+01:00
Add quickcheck subcommand (PR #406)
Added Makefile dependencies and test/test.pl tests.
- - - - -
4054ba5f by John Marshall at 2015-08-14T13:59:16+01:00
Reformat main samtools usage display
More whitespace, and a wider subcommand name column as there are
some longer subcommand names approaching.
- - - - -
ab561e1c by John Marshall at 2015-08-14T16:46:33+01:00
Add accidentally omitted short option [minor]
- - - - -
858b0e7c by Rob Davies at 2015-08-17T09:56:17+01:00
Improve header merging.
Add new merged_header_t struct to store state for the combined output
header. This is passed in to trans_tbl_init instead of a bam_hdr_t. It
includes hash tables which allow the presence of a @SQ SN, or @RG or @PG
ID in the output to be rapidly tested. It also includes separate kstrings
for the various record types, which makes it easier to get the desired
ordering of records in the combined header.
The monolithic trans_tbl_init function is broken up into smaller parts that
handle the different record types, and rewritten to use the new
merged_header_t struct. A couple of combined functions deal with the RG
and PG records, eliminating some duplicated code.
pretty_header, regex_escape and copy_headers are removed as they are no
longer needed.
New functions init_merged_header and free_merged_header are added to create
and tear doen the merged_header_t struct, along with finish_merged_header
which creates a bam_hdr_t from the data in the merged_header_t. This
effectively replaces pretty_header.
bam_translate prints warnings to stderr about tags that do not appear in
the header. It now tracks which ones it has warned about so it only
prints one message for each combination of ID and input file.
test_trans_tbl_init.c is modified to work with the new merged_header_t
struct. A lot of duplicated code is also eliminated, especially from
the setup_test_ functions.
As pretty_header has gone, test_pretty_header is no longer needed and also
removed.
test/merge/3.merge.expected.err is changed to reflect the changed
warning message from bam_translate.
- - - - -
d946f49b by James Bonfield at 2015-08-17T10:44:59+01:00
Reheader: added explicit version 2.1 and 3.0 cram tests as the code
has specific functions for each version.
- - - - -
28772779 by James Bonfield at 2015-08-17T10:53:30+01:00
Improved test harness to report the errors
...produced when a command fails to run. Otherwise it's very hard
to tell why a Travis build didn't work unless we can reproduce it.
- - - - -
3c2003ea by John Marshall at 2015-08-17T10:57:48+01:00
Merge separate CRAM v2.1 and v3.0 reheader tests
- - - - -
49ed7549 by James Bonfield at 2015-08-17T11:13:14+01:00
Made samtools cat work, when possible, with CRAM files.
The cram variant is subtly different in that where possible it
reconstructs the joint header by stitching the @RG lines from the
concatenated files, but the -h option is still available.
Changed it so it works with 1 file. It's a bit esoteric, but
technically there is no reason why it requires 2. (Unix cat copes
with 1 just fine.)
Also fixed a small memory leak in reheader.
- - - - -
8a7a1e7d by James Bonfield at 2015-08-17T11:13:14+01:00
Fixed samtools cat crash when given invalid filenames.
- - - - -
9f4d3610 by James Bonfield at 2015-08-17T11:13:14+01:00
Added CRAM tests for samtools cat.
- - - - -
7ba7dc32 by John Marshall at 2015-08-17T16:55:41+01:00
Use hts_get_format() accessor function
- - - - -
08df3db1 by John Marshall at 2015-08-17T17:08:27+01:00
Merge samtools cat for CRAM files (PR #420, #451)
Updated bam_cat.o dependencies.
- - - - -
71906070 by Rob Davies at 2015-08-18T09:34:26+01:00
Replace regex searches with dedicated match function.
Glibc's regexec calls strlen, which makes it very slow on long inputs.
Replacing it with a function that only inspects the parts of the input
text that it needs to gives a big speed-up for large headers.
- - - - -
226cb15e by Rob Davies at 2015-08-18T11:40:02+01:00
Deal with out of order @SQ lines.
@SQ lines should really be in the same order as the entries in the
binary header. Instead of adding them each time a new one is found,
record the position and add the lines in the same order as that in the
binary header at the end. This ensures the ordering even if the input
files are incorrect.
- - - - -
5edde1e2 by Shane McCarthy at 2015-08-18T12:22:54+01:00
skip first bin for AD and DPR calculations as this stores the totals for the site
- - - - -
0c5617ec by John Marshall at 2015-08-18T14:21:43+01:00
Merge mpileup updates for VCF v4.3 (PR #448)
[NEWS]
* 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
- - - - -
df82d58a by John Marshall at 2015-08-20T08:43:25+01:00
Rename hash to c2stats to reflect previous intptr->stat_t* [minor]
- - - - -
e55418f8 by John Marshall at 2015-08-20T10:09:05+01:00
Prefix errors with "samtools <subcmd>:" rather than "samtools:"
When several samtools commands are being piped into each other,
this improves the chance of knowing which one is complaining.
Also flush stdout (stderr) before (afterwards) as recommended by
https://utcc.utoronto.ca/~cks/space/blog/programming/HowToWriteToStderr
This makes a real difference in the "samtools foo >out 2>&1" case.
- - - - -
dce3c288 by John Marshall at 2015-08-20T13:32:47+01:00
Merge header merge non-regex-based rewrite (PR #453)
Finish removal of test_pretty_header.
[NEWS]
* Merging files with millions of headers now completes in a reasonable
amount of time (#337, #373, #419, #453; thanks to Nathan Weeks,
Chris Smowton, Martin Pollard, Rob Davies)
- - - - -
8be7f04b by John Marshall at 2015-08-21T10:15:42+01:00
Merge James's wgsim bug fixes
Bump version number to 0.3.2, beyond any wgsim version number in this
samtools repository or in github.com/lh3/wgsim.
- - - - -
8e3e23f8 by Kevin Murray at 2015-08-21T10:27:22+01:00
Add manpage for wgsim
Fixed man page typo. Updated copyright to match source.
Tidied up .TH. Removed version numbers from this simple man page,
so there's one less place to update with releases.
- - - - -
d779e259 by James Bonfield at 2015-08-21T10:33:35+01:00
Merged wgsim_eval.pl with
https://github.com/lh3/wgsim/commits/master/wgsim_eval.pl
(Author: lh3, but no common git history to work on.)
- - - - -
4bfd6118 by James Bonfield at 2015-08-21T10:33:36+01:00
Added some help to wgsim alneval.
Feel free to add documentation of -c. It was in the original code, but
silently removed in a later revision (by Heng)? I left it in during
merging but aren't sure what it does. So it's undocumented and hidden
for now; left in for compatibility only.
- - - - -
8e9b6f95 by James Bonfield at 2015-08-21T10:33:36+01:00
Tidied up white space to be consistent across entire file.
(It's not consistent with all other perl scripts here because there is
no consistency between them.)
- - - - -
7e4b541c by Karel Brinda at 2015-08-21T10:40:16+01:00
Support for X and = in CIGAR strings
[Cherry-picked PR lh3/wgsim#6.]
- - - - -
ea5a92f7 by John Marshall at 2015-08-21T10:50:31+01:00
Merge misc/wgsim updates and man page (PR #428)
- - - - -
881e2249 by John Marshall at 2015-08-24T10:22:13+01:00
Rename split option -T/--tag-split to -S/--split
Add samtools.1 documentation, and remove -s/--sam documentation (input
format is always auto-detected). Simplify split_tag option handling.
- - - - -
f0cb72c7 by Martin O. Pollard at 2015-08-24T11:19:13+01:00
Split out bam1_t to fastq processing and add option to output to files.
Add -1 and -2 options to output FASTQ to files instead of STDOUT.
Separate out bam1_t to fastq processing step and make it self contained.
Add options to filter reads by flags.
Signed-off-by: Martin O. Pollard <mp15 at sanger.ac.uk>
- - - - -
289ae950 by Martin O. Pollard at 2015-08-24T11:19:27+01:00
Comments to explain bam2fq mainloop
Add some comments to explain two stage output of main loop.
Signed-off-by: Martin O. Pollard <mp15 at sanger.ac.uk>
- - - - -
20b5b13d by Martin O. Pollard at 2015-08-24T12:53:33+01:00
Refactor bam2fq arg parsing and init
Move argument parsing for bam2fq out of main.
Move state initialisation for bam2fq out of main.
- - - - -
e762eec6 by Martin O. Pollard at 2015-08-24T12:58:23+01:00
Add comments to bam2fq mainloop
Add comments to bamtofastq mainloop.
Convert readpart to enum
- - - - -
50ad1b54 by Martin O. Pollard at 2015-08-24T13:07:36+01:00
Rewrite branch 'bam2fq_format' of github.com:peterjc/samtools into bam2fq_improve
Don't mix FASTQ and FASTA in output.
Add default quality where reads don't have quality.
Reimplemented to fit into current bam2fq working branch. Hat-tip to Peter J Cock for original.
- - - - -
dbea8497 by John Marshall at 2015-08-24T15:41:05+01:00
Merge samtools stats splitting (PR #421)
- - - - -
8d792d2f by James Bonfield at 2015-08-25T09:21:43+01:00
Inverse video mode for tview and also changed some colours.
Fixes #457
- - - - -
1849a6ec by James Bonfield at 2015-08-25T10:07:21+01:00
Fixed wgsim so that it doesn't have infinite loops if it finds a sequence of Ns.
Sorry about the use of goto, but I find it clearer than reversing the
incrementer phase so the for loop inc becomes a nop; especially now it
needs a reset of max_loop.
- - - - -
b73d36e9 by Martin O. Pollard at 2015-08-25T10:19:55+01:00
Rewrite of bam2fq singleton tracking with tests
Squashed several abortive attempts into this commit for a simplified merge
Rewrite singleton tracking into simpler form based on John Marshall's pseudo code
Add tests to new bam2fq codepaths
Add test to -1 and -2 options for bam2fq.
Fix fclose return value stupidity
Add tests to exercise the BAM_FSECONDARY|BAM_FSUPPLEMENTARY code paths
Changed double pointer of fpr to array of 3 pointers.
Changed r0,r1,r2 into an array of 3 pointers.
Reordered and tweaked usage message to match up with new style.
- - - - -
6a22b4f3 by Martin O. Pollard at 2015-08-25T10:23:16+01:00
Rename bam2fq to fastq and fasta respectively
- - - - -
3c0e3a5a by Sam Nicholls at 2015-08-25T11:52:30+02:00
Add stats split prefix support and split indicator
* Add `-P`, `--split-prefix` to `samtools stats` to prepend
filenames created by `-S` or `--split` with a path or string.
* Add an additional comment line at the head of `samtools stats`
output to clarify whether the statistics pertain to all or
a tagged subset of reads.
- - - - -
f75eb347 by James Bonfield at 2015-08-25T12:24:51+01:00
Calmd now accpets the global I/O options.
Note that this is largely pointless on CRAM except for the unlikely
case of a CRAM file built with the no_ref option.
Also fixed a crash when the specified reference file cannot be
loaded.
- - - - -
8123d021 by James Bonfield at 2015-08-25T14:21:20+01:00
Minimal fix to make --reference replace -f fasta_ref when not
explicitly specified.
- - - - -
55203720 by James Bonfield at 2015-08-25T14:30:23+01:00
Tview now uses --reference value if specified (and ref not manually specified)
- - - - -
77761c37 by James Bonfield at 2015-08-25T14:35:51+01:00
Added depad to help output.
I think we fixed the bugs, so I don't believe it's any more unstable
than other tools. Plus it's in the man page already.
- - - - -
cf18e414 by James Bonfield at 2015-08-25T17:28:57+01:00
Added global i/o options to "samtools depad".
- - - - -
3ab5f6c4 by James Bonfield at 2015-08-26T12:25:48+01:00
Made targetcut -f and --reference the same option.
- - - - -
8f3e729b by John Marshall at 2015-08-26T13:41:41+01:00
Have stats --split-prefix set the output prefix rather than adding to it
Previously "samtools stats -P foo/bar -S RG data/seq.bam" would try to
write to foo/bardata/seq.bam_<rg>.bamstat, and likely collapse because
foo/bardata doesn't exist. Better if we write to foo/bar_<rg>.bamstat as
that doesn't involve any directories not obviously specified by the user.
- - - - -
3e9357c3 by John Marshall at 2015-08-26T13:53:56+01:00
Merge stats split output filename prefix (PR #460)
Alphabetised man page and usage options.
Fix misc/wgsim.c whitespace [trivial].
- - - - -
13de48f8 by James Bonfield at 2015-08-26T16:21:00+01:00
Added a bam_get_library() implementation.
Needed by rmdup and view. Also resolves 6 of our expected failures.
- - - - -
fff21fe5 by James Bonfield at 2015-08-26T16:25:19+01:00
Updated the rmdup command to use the newer htslib interface instead of
the old bam.h one.
Also added the new I/O long-options.
Finally, due to the previous addition of bam_get_library(), this is
now "working" for the first time since 0.1.x series.
- - - - -
77c8b4e5 by James Bonfield at 2015-08-26T16:45:15+01:00
Added recently changed #include dependencies to Makefile.
- - - - -
25bee0e1 by James Bonfield at 2015-08-26T17:55:15+01:00
Added calls to sam_open_mode() to auto-detect file format by name.
This fixes the output for fixmate, rmdup, merge, sort and depad. Note
it does not change the behaviour of samtools view -o FILE as I believe
this didn't previously auto-detect format, but it's trivial to add
that too if required.
- - - - -
5b3280d2 by John Marshall at 2015-08-27T23:58:59+01:00
Document make targets to build htslib utilities
$(HTSDIR)/htslib.mk now supplies both all-htslib and install-htslib
targets. Fixes #462.
- - - - -
2bd7837f by Sam Nicholls at 2015-08-28T16:16:44+02:00
Update stats --split-prefix usage to match 8f3e729
- - - - -
4d2efe93 by John Marshall at 2015-09-01T13:44:31+01:00
Use kstring's kgetline()
[stats.c] Remove mygetline() in favour of kgetline(). Closes #383.
[test/**.c] Use kgetline() instead of getline(). Fixes #392.
- - - - -
fcaafe04 by James Bonfield at 2015-09-01T17:39:18+01:00
Merge pull request #459 from samtools/tview_colours
Inverse video mode for tview and also changed some colours.
- - - - -
11ccd2a3 by James Bonfield at 2015-09-04T11:43:51+01:00
Added -o/-U filename.<suffix> detection to samtools view.
Also fixed a bug where using -C and -U together failed due to not
specifying the reference to the -U cram file.
The suffix used can differ between -o and -U. The format is
overridden by -b / -c or --output-fmt. It is not possible to specify
a different format for -o and -U except via suffix guessing (this was
not possible previously either as there is only a single -b/u/C
option).
- - - - -
495b86cd by John Marshall at 2015-09-07T13:15:54+01:00
Add missing Makefile dependencies
Remove bam_pileup.o, which was removed in e7ae7f96c7e78a2dd6eabdaed57037c483951929.
- - - - -
093192e2 by John Marshall at 2015-09-07T13:23:11+01:00
Canonicalise Makefile dependencies [minor]
Reorder prerequisites to the same order as #include lines in the source
file, which facilitates automatically generating these dependencies.
- - - - -
3978ecae by Martin O. Pollard at 2015-09-07T13:30:09+01:00
Fixup bam2fq true and false, update copyright dates and man page.
Man page had old command names on it, update them.
Make true success and false failure for our functions.
Update copyright dates on test SAM because changes core to what
they're about were made when these derived works were created.
- - - - -
af76b1ae by John Marshall at 2015-09-08T16:23:12+01:00
Reformat calmd_usage() to 2-space option indentation
- - - - -
caea8016 by John Marshall at 2015-09-09T17:26:00+01:00
Merge --output-fmt-option etc followup (PR #461)
Update copyright years in bam.c, bam_rmdup.c, bam_rmdupse.c.
Use HTSlib's bam_endpos() instead of bam_calend() in bam_rmdupse.c.
[NEWS]
* 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 [#159, #252, #291, #393]
- - - - -
e0306d25 by Martin O. Pollard at 2015-09-11T09:09:29+01:00
Port addreplacerg command over from separate repo
Port command to add or replace readgroups in BAM/CRAM over from standalone repository.
Signed-off-by: Martin O. Pollard <mp15 at sanger.ac.uk>
- - - - -
0bd5498c by Martin O. Pollard at 2015-09-11T09:09:30+01:00
Add ability to add new RG to file.
Rework command line options.
Allow choice between overwriting all tags or only those where no
existing RG tag exists.
Signed-off-by: Martin O. Pollard <mp15 at sanger.ac.uk>
- - - - -
74b4c594 by Martin O. Pollard at 2015-09-11T09:09:30+01:00
Add long input and output format options to addreplacerg
-Adapt code to use new input/output formating options
- - - - -
9a8f2f6d by Martin O. Pollard at 2015-09-11T09:09:36+01:00
Fixes for addrprg based on @jmarshall's review
Fix man page.
Const init param pointer.
Do not unescape \n's.
Remove old mode format craft.
Convert to more conventional readloop.
Add alternate -r syntax.
Tweak documentation for addreplacerp.
By default write to stdout and add a -o option.
- - - - -
798c7bc6 by Sam Nicholls at 2015-09-11T09:09:36+01:00
Correct stated default mode for addreplacerg
- - - - -
93973873 by Martin O. Pollard at 2015-09-11T09:09:37+01:00
addreplacerg style fixes, usage correction and bugfix
Fix where in file was being set by the -o option.
Update usage to add -o
Update man page to change input.srt.bam to input.bam
Fix memory leak in parse_opts
Update to new print_error_errno syntax
- - - - -
17a8d790 by Martin O. Pollard at 2015-09-11T13:21:52+01:00
Fix addrprg entertaining off by one error, spec valid but breaks stuff
l_text in header according to the spec can include '\0' however this breaks some parsers.
- - - - -
2f148b15 by Afif Elghraoui at 2015-09-13T18:49:19-07:00
Set up a new changelog entry
- - - - -
eb569180 by Afif Elghraoui at 2015-09-13T18:51:50-07:00
Add patch to fix building on i386
- - - - -
702d2892 by Afif Elghraoui at 2015-09-13T21:08:18-07:00
Remove source files not present in upstream tarball
I'm not sure how they got there, but they cause problems
when building the package.
- - - - -
7afd302d by Afif Elghraoui at 2015-09-13T22:19:17-07:00
Allow all scripts to be called without language extensions
- - - - -
c6cefd5c by Afif Elghraoui at 2015-09-13T22:22:04-07:00
Update changelog for 1.2-2 release
- - - - -
c76e08da by Afif Elghraoui at 2015-09-13T22:29:26-07:00
Mark release and remove redundant changelog entry
- - - - -
7c4cce46 by John Marshall at 2015-09-15T15:46:01+01:00
Add addreplacerg command (PR #371)
[NEWS]
* New addreplacerg command that adds or alters @RG headers and RG:Z record tags
- - - - -
c740a12b by Charles Plessy at 2015-09-16T18:02:31+09:00
Revert "Remove source files not present in upstream tarball"
This reverts commit 702d28926f97b3acb9ce92705cbbe28b41015615.
- - - - -
876f680f by Charles Plessy at 2015-09-17T20:18:41+09:00
Note that this source package is managed like htslib.
This message should point to the Debian Med Policy once it is updated.
- - - - -
6691fed2 by Charles Plessy at 2015-09-17T20:23:10+09:00
samtools (1.2-2) unstable; urgency=medium
[ Afif Elghraoui ]
eb56918 Add patch to fix building on i386
702d289 Remove source files not present in upstream tarball
7afd302 Allow all scripts to be called without language extensions
[ Charles Plessy ]
876f680 Document the update workflow of the source package's repository.
-- Charles Plessy <plessy at debian.org> Thu, 17 Sep 2015 20:21:15 +0900
- - - - -
dffc67f3 by Benjamin Schuster-Boeckler at 2015-09-17T15:17:31+01:00
Added code to fix #343, thanks @cyrusmaher for the pointer in the right direction
- - - - -
19de55ee by Afif Elghraoui at 2015-09-22T06:39:58-07:00
Revert "Allow all scripts to be called without language extensions"
This reverts commit 7afd302dc02a8c4521017b68a3db4063ff86c4ac.
Closes: #799698
- - - - -
658179c6 by Afif Elghraoui at 2015-09-22T06:41:10-07:00
Revert "Remove source files not present in upstream tarball"
This reverts commit 702d28926f97b3acb9ce92705cbbe28b41015615.
This does not really cause a major problem.
- - - - -
06626640 by Afif Elghraoui at 2015-09-22T06:54:59-07:00
Prepare for upload
- - - - -
32bbc451 by Andreas Tille at 2015-09-22T16:17:26+02:00
Fix synopsis and vcs-browser
- - - - -
477fe990 by Andreas Tille at 2015-09-22T16:22:47+02:00
Add lintian-override to document that the language extensions are used internally
- - - - -
8a507bc2 by Andreas Tille at 2015-09-22T16:23:33+02:00
Fix spelling
- - - - -
9f6248cb by Andreas Tille at 2015-09-22T16:24:22+02:00
Mark as team upload since I do not intend to become Uploader for samtools
- - - - -
56c94373 by John Marshall at 2015-10-07T14:05:39+01:00
Fix typo in conditional [minor]
Also minor nearby style: use INT_MAX for position infinity rather
than 1<<29 or 0x7fffmagic; free() handles NULL pointers itself.
- - - - -
e066deb7 by Rob Davies at 2015-10-07T16:33:37+01:00
Make merge allow input files with no @HD line
Remove check added in 55c852f that required the first SAM header to have an
@HD line when merging. Previous versions worked if no @HD lines were
present; this allows the new header merge code to do so as well.
The new behaviour is that the first @HD line found on either the file
given in the '-h' option, or any of the input files, will be used. If no
@HD line is found the program will complain, but it will continue and
exit successfully (assuming it otherwise worked).
Some code is included to add an @HD if none was present on the inputs, but
it's currently commented out pending discussion.
Fixes #475
- - - - -
f44f54d2 by John Marshall at 2015-10-08T14:21:33+01:00
Miscellaneous tidy-ups [minor]
Update sam_view.c copyright year. Reformat usage. Remove debugging
"Producing XYZ output" (which appeared even for usage displays).
Update usage and samtools.1 synopsis lines to "[options]" now that there
are lots of options beyond the original few.
Write test/test.pl flag filter clearly.
- - - - -
834bf7e9 by John Marshall at 2015-10-08T15:47:12+01:00
Merge bam2fq improvements (PR #263)
- - - - -
6e4bc524 by James Bonfield at 2015-10-12T15:02:35+01:00
Merge pull request #476 from daviesrob/merge_no_hd
Make merge allow input files with no @HD line
- - - - -
87cdc4a9 by John Marshall at 2015-10-20T13:58:19+01:00
Define and use .EX/.EE macros for examples and code blocks
Removes filling and hyphenation from code examples, formats in Courier
in PS output, and paves the way for <pre>-style formatting on conversion
to HTML. Hat tip @kbradnam. The macros are intentionally named similarly
to Ultrix's similar man macros.
Also add '\" preprocessors-needed header line.
- - - - -
370c7ea2 by John Marshall at 2015-11-11T13:15:23+00:00
Merge develop's --output-fmt-option changes in bam_sort()
Both this branch (fmtout etc) and later changes on the develop branch
handle -O and format setting in their own ways. This handling is currently
duplicated in this merge and will be fixed clearly in a later commit.
- - - - -
7f2bc8ed by John Marshall at 2015-11-18T16:48:23+00:00
Update legacy-attempt heuristics and diagnostics
Remove this branch's format setting code, as this is already handled
by the code merged in from the develop branch.
Remove "-o followed by another option" heuristic as the scenario it
handles (legacy "-o -n in.bam tmp") is always already detected by the
"legacy <out.prefix>" test.
Add heuristic to detect legacy "-o in.bam tmp", to the extent that can
be distinguished from modern "-o out.bam in.bam" (namely opening "tmp"
for reading fails and it doesn't have a .bam/etc extension).
Note the historic usage and how to move away from it in the man page.
Add obsolete invocation test cases.
- - - - -
d637d596 by John Marshall at 2015-11-18T17:03:57+00:00
Avoid memory leaks on invocation error abends
- - - - -
a9972058 by John Marshall at 2015-11-20T10:49:42+00:00
Merge legacy sort usage removal (PR #441)
[NEWS]
* 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. (#295, #349, #356, #418, PR#441; see also
discussions in #171, #213)
- - - - -
40404966 by Shane McCarthy at 2015-11-20T14:00:30+00:00
Document "*" region query for unmapped read pairs
(Use bold instead of extra quoting to avoid confusion for '*', which
needs to be quoted on the command line.)
- - - - -
3af0bec6 by John Marshall at 2015-11-20T14:25:11+00:00
Describe $HTS_PATH, the search path for HTSlib plugins
- - - - -
f2c357cb by John Marshall at 2015-11-20T15:43:07+00:00
Reformat merge usage
- - - - -
fe1868b0 by Martin O. Pollard at 2015-11-20T16:13:54+00:00
Update merge -cp usage
Update merge -cp usage to clarify we use the first line with a given ID
rather than merging the actual lines (fixes #482)
- - - - -
4d564373 by John Marshall at 2015-11-26T17:24:52+00:00
Improve error messages for opening or format errors
Take advantage of samtools/htslib at 6462e349d16e83db8647272e4b98d2a92992071f.
- - - - -
97c9883e by Martin O. Pollard at 2015-12-08T15:09:23+00:00
Rename bamshuf to collate
Now that bamshuf can handle CRAM files we have renamed it so that
it has a more appropriate name.
[NEWS]
* 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)
- - - - -
90dcd901 by John Marshall at 2015-12-09T12:27:29+00:00
Allow for n_targets==0 in finish_merged_header() shrinking
The realloc() function might return NULL when asked to resize to zero
bytes. It is near impossible to correctly distinguish NULL-as-resize-0
(incoming ptr freed) and NULL-as-realloc-failed (incoming ptr not freed):
see WG14 defect report 400 and Austin Group issues 400, 526, and 688.
Avoid all this by simply setting target_name and target_len to NULL when
n_targets==0, leaving merged_hdr->target_name/len to be freed later by
free_merged_header().
Fixes #495. Hat tip to @daviesrob for identifying the cause.
- - - - -
803143bf by James Bonfield at 2015-12-14T12:24:11+00:00
Made --threads long option versions of - at .
(Rebased from PR #472.)
- - - - -
defd753b by John Marshall at 2015-12-14T13:11:37+00:00
Use $(htslib_kfoo_h) make variables for htslib/k* headers
Using these variables allows them to be empty when samtools is compiled
against an installed htslib rather than a development htslib.
See also samtools/htslib at 90525e00acb218a6b047eff08473c92f2ef3ec6e.
- - - - -
ea6d10c8 by John Marshall at 2015-12-15T17:44:11+00:00
Add configure.ac script
Use autoconf to generate a configure script. Searches for your HTSlib
source tree or installation (fixes #275, fixes #414), checks for curses,
zlib, etc, and emits hopefully informative errors if anything is missing.
Split $(HTSLIB) into $(HTSLIB) (for prerequisites) and $(HTSLIB_LIB) (for
link commands) so that they can be different (empty, -lhts) for building
against an installed HTSlib.
Unconditionally include config.mk from the Makefile, and add rules to
generate basic config.mk/.h (using ../htslib as before) if configure has
not been run. This don't-need-to-use-configure mode will likely disappear
in the near future.
Use AX_WITH_CURSES to detect curses flavour, including determining the
name of the library to link against. Fixes #269, fixes #346, hopefully
improves #66. Add config.h to bam_tview_curses.c; (TODO) eventually it
should be included by all C files, but at the moment config.h contains
only curses-related defines.
AX_WITH_CURSES is from autoconf-archive, and AX_WITH_HTSLIB will soon be
submitted there.
Providing install-sh is a prerequisite for AC_CONFIG_SUBDIRS, which
AX_WITH_HTSLIB uses. (TODO) Use AC_PROG_INSTALL to set $(INSTALL) et al.
(This is the current install-sh from Gnulib.)
(TODO) Update INSTALL and other documentation.
[NEWS]
* Samtools now has a configure script which checks your build environment
and facilitates choosing which HTSlib to build against. See INSTALL
for details
- - - - -
3c15c88a by John Marshall at 2015-12-15T17:44:15+00:00
Always link with -rdynamic/-ldl [hack]
As a quick hack to make plain "make" work in both typical HTSlib
scenarios (plain HTSlib; HTSlib configured with --enable-plugins),
add -rdynamic and -ldl to link commands ALWAYS. In future, we would
prefer to communicate the exact linking needs from HTSlib via perhaps
htslib.pc and/or more configure delving.
Introduce $(ALL_LIBS), which will outlast this hack being reverted.
- - - - -
4b4e6880 by John Marshall at 2015-12-15T17:44:28+00:00
Update INSTALL etc to discuss configuring samtools
- - - - -
ed3191b1 by John Marshall at 2015-12-15T21:26:20+00:00
Samtools release 1.3: many improvements, bug fixes, and new commands
- - - - -
493b1ca6 by John Marshall at 2015-12-15T23:14:27+00:00
Merge version number bump and NEWS file from master
- - - - -
3c197df8 by María de Antón at 2015-12-18T17:10:56+00:00
set a matrix.include for all os options
- - - - -
0777f642 by Andreas Tille at 2015-12-21T13:24:01+01:00
Fix Mayhem issues caused by unlimited reads of gz input
- - - - -
95188c1f by Andreas Tille at 2015-12-21T13:48:54+01:00
Provide some more manpages
- - - - -
663b1a8e by Andreas Tille at 2015-12-21T13:49:12+01:00
Upload to unstable
- - - - -
4a5274b4 by Charles Plessy at 2015-12-24T13:50:30+09:00
Merge branch 'debian/unstable' of git+ssh://git.debian.org/git/debian-med/samtools into debian/unstable
- - - - -
95c561dc by Charles Plessy at 2015-12-24T13:55:19+09:00
Merge tag '1.3' into debian/unstable
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. (#295, #349, #356, #418, PR #441; see also
discussions in #171, #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; #79, #125, #286, #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 (#159, #252, #291, #393).
* Merging files with millions of headers now completes in a reasonable
amount of time (#337, #373, #419, #453; thanks to Nathan Weeks,
Chris Smowton, Martin Pollard, Rob Davies).
* Samtools index's optional index output path argument works again (#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 (#457).
* Samtools depad command now handles CIGAR N operators and accepts
CRAM files (#201, #404).
* Samtools stats now outputs separate "N" and "other" columns in the
ACGT content per cycle section (#376).
* Added -a option to samtools depth to show all locations, including
zero depth sites (#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 #269, #305, #320, #328, #346, #353, #365, #392, #410, #445,
#462, #475, and #495.
- - - - -
824f68f0 by Charles Plessy at 2015-12-24T13:59:30+09:00
New upstream release; no new copyright nor license notice.
- - - - -
86a93751 by Charles Plessy at 2015-12-24T14:02:04+09:00
Replace LDLIBS by LIBS, following upstream changelog.
- - - - -
c12f4f35 by Charles Plessy at 2015-12-24T14:08:27+09:00
Removed patch; issue solved upstream.
https://github.com/samtools/samtools/pull/286
- - - - -
5c4ca0b5 by Charles Plessy at 2015-12-24T14:09:58+09:00
Removed patch; issue solved upstream.
https://github.com/samtools/samtools/issues/305
- - - - -
befba2ea by John Marshall at 2015-12-31T13:07:37+13:00
Include <unistd.h> for isatty() [minor]
We get <unistd.h> as a byproduct of zlib.h and getopt.h on Linux and OS X,
but not on FreeBSD.
- - - - -
de68be6c by John Marshall at 2016-01-03T09:19:41+13:00
Happy New Year
- - - - -
664cc5fe by James Bonfield at 2016-01-05T00:01:26+13:00
Fixed a known-failure (mpileup -d) issue; now passes.
samtools/htslib at df4a80e9c387bb1d84cdb47c02e44e77b0f57770 has removed a
dummy field from the pileup structure. In doing so this decrements the
number of items in the mp pool by 1, which coincidentally was the cause
of the maximum depth field being out by one. Bonus!
- - - - -
74a3e0a7 by John Marshall at 2016-01-28T10:56:56+00:00
Add #include <config.h> to all *.c source files [minor]
Upcoming config.h settings will have ODR implications, so ensure all
source code sees these settings.
Also add missing faidx.o rule.
- - - - -
4988ce7a by Sascha Steinbiss at 2016-01-30T21:23:51+00:00
adapt to new build system
- - - - -
45397bc4 by Sascha Steinbiss at 2016-01-30T21:23:51+00:00
use secure Vcs-Git
- - - - -
f1e3f7c8 by Sascha Steinbiss at 2016-01-30T21:23:52+00:00
patch configure.in to not call make in m4_esyscmd_s()
- - - - -
6479cce7 by Sascha Steinbiss at 2016-01-30T21:23:52+00:00
add Build-Dep to automake
- - - - -
487e759e by Sascha Steinbiss at 2016-01-30T21:23:53+00:00
cleanup copyright
- - - - -
d985799b by Sascha Steinbiss at 2016-01-30T21:31:14+00:00
add patch header
- - - - -
82f34d34 by Sascha Steinbiss at 2016-01-30T21:38:54+00:00
patch spelling
- - - - -
59ab663f by Martin Pollard at 2016-02-02T13:34:15+00:00
Fix -O option for reads without OQ tag
When using the -O option the +1 meant our NULL check was failing. Fix to only
populate oq variable where there is an OQ tag present. Fixes #517
- - - - -
03a6bc5b by James Bonfield at 2016-02-02T14:12:21+00:00
Improved documentation of mpileup -l vs -r.
Fixes #128 and #130.
- - - - -
9d12a17a by Sascha Steinbiss at 2016-02-03T10:13:39+00:00
update d/changelog
- - - - -
a9bf06a3 by Sascha Steinbiss at 2016-02-05T08:29:26+00:00
add NEWS for 1.3 commandline API changes
- - - - -
096bc417 by Sascha Steinbiss at 2016-02-05T08:32:52+00:00
dch -r
- - - - -
23b91e87 by James Bonfield at 2016-02-05T17:26:12+00:00
Improved documentation of how mpileup -d/-L work.
They're still quirky, but at least it's documented quirks!
- - - - -
a5cdff68 by Ben Taylor at 2016-02-08T14:45:45+00:00
Remove gcc build on OSX
It's just using clang anyway:
https://travis-ci.org/samtools/samtools/jobs/107289030#L37
- - - - -
c6131472 by James Bonfield at 2016-02-09T15:13:24+00:00
Tidied up the mpileup.[123].sam files to not use RNAME fields with no @SQ records.
I could have added the entries to the @SQ records, but this may have
caused more problems given we don't have the full chr17, just 4200
bytes of it and the mini-sequence in the ref.fa file. Side-stepping
the whole CRAM and reference-required issue is the route of least
resistance.
Fixes #489
- - - - -
c152c47b by James Bonfield at 2016-02-11T11:20:17+00:00
Fix typo.
- - - - -
3d792baf by James Bonfield at 2016-02-11T11:21:07+00:00
Merge pull request #525 from samtools/mpileup_depth
Improved documentation of how mpileup -d/-L work.
- - - - -
bf854402 by James Bonfield at 2016-02-11T12:04:17+00:00
Grammar fix.
- - - - -
dae373be by John Marshall at 2016-02-11T14:27:54+00:00
Ignore .exe extension; don't force core and ~ ignorance
Some developers prefer not to have core and *~ be ignored, and
settings here in .gitignore cannot be overridden. Those who do
want them ignored should add local entries in $GIT_DIR/info/exclude
or in their core.excludesfile.
(Remove /bgzip entry, which has long since moved to htslib.)
- - - - -
ac5b8e7c by John Marshall at 2016-02-11T15:54:04+00:00
Use AC_SYS_LARGEFILE configure test instead of -D_FILE_OFFSET_BITS=64
Defines _FILE_OFFSET_BITS etc in config.h as appropriate. On 64-bit
machines we don't need it, and it was just noise in make log output.
On 32-bit machines it now exactly parallels the settings applied in
HTSlib post samtools/htslib at f1327a703583bf61e2e7ffd11198487fee2a8422.
On 32-bit machines it is now *required* to run configure in order for
large files to be usable. But it'll likely soon be non-optional for
everyone anyway.
- - - - -
ce44eb37 by Martin Pollard at 2016-02-16T15:28:26+00:00
Add check on hts_close to quickcheck
Add check on hts_close to quickcheck command, we are missing some errors here.
Add expected_fail test for CRAM file missing EOF block.
[JM: Add to quickcheck/all test, with expected_fail.]
- - - - -
6e3ac270 by James Bonfield at 2016-02-17T12:18:03+00:00
Fixed bam_get_library() crash.
This was triggerable from samtools rmdup or samtools view -l when an
@RG header was present without an LB: record.
I also fixed the samtools view -l logic. The man page states that it
only shows reads in that library, while the implementation was to only
show reads in that library or those where it could not determine the
library.
Fixes #538
- - - - -
2dcdd620 by Joshua C. Randall at 2016-02-22T15:51:06+00:00
Adds a usage note to `samtools quickcheck`
- - - - -
d49c73b9 by John Marshall at 2016-02-22T16:16:28+00:00
Reformat "Notes" in long -? usage output
Make code examples stand out more. Drop excess `foo' and `bar` quoting.
Use 'fail!' rather than "fail!" as the latter invokes the history mechanism
in Bash.
- - - - -
3c8a69f0 by John Marshall at 2016-02-23T14:35:22+00:00
Fix samtools merge -n usage doc [minor]
- - - - -
de96bfb6 by Rob Davies at 2016-03-08T14:22:46+00:00
Fix warnings from adding HTS_RESULT_USED to htslib prototypes.
Companion to PR samtools/htslib#271. Add checks to return values from
functions now marked with HTS_RESULT_USED in htslib. Also fix some other
obvious places where errors were not handled correctly. Try to improve
cleanup code so that memory is not leaked and files are closed, even when
exiting due to an error.
- - - - -
0e260d91 by Rob Davies at 2016-03-08T14:35:23+00:00
Ensure fp is always closed in write_buffer.
Prevents file descriptor leak on errors. Hat tip to
godotgildor's pull request https://github.com/samtools/samtools/pull/253
which is duplicated in this patch. I would have merged it in if I'd
noticed it earlier...
- - - - -
f63a2822 by John Marshall at 2016-04-01T15:01:42+01:00
Recreate missing @SQ header from BAM binary header
Some tools create BAM files with no text @SQ headers, which is unusual
but nonetheless valid. Create a basic dummy header from the binary
header, as we may be merging with another file that does have @SQ
headers and having some but not all is not valid.
Fixes #548 and fixes #550.
- - - - -
cd7e0051 by John Marshall at 2016-04-03T10:16:57+01:00
Fix indentation [minor]
Hat tip @zfrenchee.
- - - - -
3baa47bc by Shane McCarthy at 2016-04-06T09:04:07+01:00
manpage: fix typo [minor]
- - - - -
09dda53c by Shane McCarthy at 2016-04-06T09:06:19+01:00
fastx: only show relevant usage options for fasta/fastq commands
- - - - -
33122256 by John Marshall at 2016-04-06T11:34:12+01:00
Merge fasta usage message improvements (PR #555)
(Hopefully simpler with multiple printfs.)
- - - - -
6994f30a by Martin O. Pollard at 2016-04-07T10:37:21+01:00
Check sam_read1() return value correctly
BAM returns different values to SAM and there was a silly mistake in
the code that checked that value. (Fixes #532)
- - - - -
54a91c14 by George Hall at 2016-04-12T15:14:38+01:00
Implemented tab completion
I have added a script which determines all Samtools subcommands and the
options available for these subcommands. It then generates a file which,
when sourced in Bash, allows for tab completion of all subcommands, and,
when appropriate, the long options for the relevant subcommand.
- - - - -
24d3235d by John Marshall at 2016-04-13T10:23:07+01:00
Use print_error_errno() where appropriate
Use it in error-checking code new to this branch and when reporting
errors from opening files (cf #51). Not used in bam_sort.c and
bam_split.c as these are also compiled into test/merge/* and
test/split/* test programs, which cannot be linked with bamtk.c.
(TODO) Move print_error()/etc to sam_opts.c, and merge samtools.h/
sam_opts.h/sam_opts.c into sam_utils.[ch] or similar.
- - - - -
fd02fc56 by George Hall at 2016-04-13T12:36:56+01:00
Dynamically generate options
As was apparently mentioned at the meeting, it is probably better to
dynamically generate tab completions rather than to generate a one-off
script which the user then stores. This is what this new version does -
possible completions for subcommands and long-options are generated
on the fly, meaning that it is no longer necessary to try and keep the
completion file up-to-date. Additionally, this allows for support of
mulitple versions etc, by append lines to the bottom of the file, as
noted in the comments.
I have removed the previous version.
- - - - -
24853450 by George Hall at 2016-04-13T14:21:25+01:00
Cleaned up subcommand name retrieval
- - - - -
193eecb5 by George Hall at 2016-04-13T14:28:58+01:00
Changed '==' to '-eq'
- - - - -
11528818 by John Marshall at 2016-04-14T14:27:56+01:00
Various tidying up and segfault fixes
bam_cat.c: fix exit status.
bam_rmdup.c: clean up even when bam_rmdup_core/bam_rmdupse_core fails.
bam_rmdupse.c: use the usual -1=>error convention.
bam_sort.c: fix new "samtools merge -f out.bam nonexistent.bam" segfault.
bamshuf.c: reuse bam1_t structs in `a`, simplifying destroying them
in case of error.
padding.c: fix existing "samtools depad nonexistent.bam" segfault,
fix exit status.
phase.c: rewrite file open loop as function, fix exit status,
(TODO) note memory/file descriptor leaks still present.
sam.c: don't bam_hdr_destroy() the user's aux; when sam_hdr_write()
fails, return NULL irrespective of bam_verbose.
- - - - -
f6db7827 by John Marshall at 2016-04-14T14:44:04+01:00
Merge error checking improvements (PR #467)
Companion to PR samtools/htslib#271. Add checks to return values from
functions now marked with HTS_RESULT_USED in htslib. Also fix some other
obvious places where errors were not handled correctly. Try to improve
cleanup code so that memory is not leaked and files are closed, even when
exiting due to an error.
Note that this introduces duplication of cleanup code (there's the
normal flow, and there's goto-fail cleanup that needs to deal with
partially-initialised data structures) in several source files.
(TODO) Large amounts of duplicated cleanup code in bam_rmdup.c,
bam_rmdupse.c, bam_sort.c, and bamshuf.c that could perhaps be
refactored to duplicate less code.
- - - - -
72679e1f by John Marshall at 2016-04-14T14:55:28+01:00
Fix \r\n thinko [minor]
- - - - -
0bfa8d42 by George Hall at 2016-04-14T16:55:32+01:00
Captialised variables for consistency
- - - - -
2389a31d by George Hall at 2016-04-15T12:51:09+01:00
Fixed slight bug in default behaviour
Now handles files with spaces in their names correctly.
In doing so, I have basically made the change mentioned here:
https://github.com/samtools/samtools/pull/560#discussion-diff-59540631 I
have made the change in a slightly different location, however, as this
has the advantage of not allowing the user to expand '/' or similar when
they should be entering a subcommand (i.e. when completing the first
argument).
- - - - -
9968e4c3 by James Bonfield at 2016-04-18T10:47:12+01:00
Make samtools sort notice when it clobbers other sorts
The temporary filenames still aren't unique; the same filenames
generated when opening and then again when unlinking, so fixing this
properly requires larger code reorganisation.
- - - - -
5f53e3cd by John Marshall at 2016-04-19T13:31:56+01:00
Propagate errno from sort worker threads
Return errno to the main thread, and on failure print it in an error
message. Improve other I/O-related error messages to show errno (cf #51).
- - - - -
b5047ab4 by James Bonfield at 2016-04-21T12:10:01+01:00
Removed a (harmless) perl warning from test harness.
- - - - -
8471a0d7 by John Marshall at 2016-04-21T14:18:58+01:00
Add `@CO` headers only once when merging sort temp files
Add MERGE_FIRST_CO for samtools sort (but don't expose it via the
merge command). When set, bam_merge_core2() will copy `@CO` headers
from only the first file to be merged, so when a large sort produces
several temporary files to be merged, the headers won't be duplicated
in the final output.
This is a quick semi-hack to fix #563; there may be better ways to
fix this with greater refactoring. See #390 for discussion of why
this simplistic approach is not suitable for samtools merge in general.
- - - - -
5839af65 by John Marshall at 2016-04-22T09:19:42+01:00
Write sort's temporary files alongside the *output* file
If several sorts are running simultaneously, the output filenames are
more likely to be distinct than the input filenames (which might often
be standard input). This is a return to the pre-PR #441 behaviour.
If -T specifies a directory or the output is standard output, add a
random component to the prefix to try to avoid collisions. (For output
to stdout with -T not specified, collisions would otherwise be certain.)
Fixes #523, fixes #535, et al.
- - - - -
897c0027 by John Marshall at 2016-04-22T10:22:44+01:00
Samtools release 1.3.1: bug fixes, notably sort temporary file fixes
- - - - -
7d3f3a8f by John Marshall at 2016-04-22T14:48:37+01:00
Merge version number bump and NEWS file from master
- - - - -
9627ffb9 by John Marshall at 2016-04-25T13:47:35+01:00
HTSlib now provides errmod_cal() etc
- - - - -
a60dd378 by John Marshall at 2016-04-26T09:48:31+01:00
Use HTSlib's new sam_prob_realn() and sam_cap_mapq() functions
Samtools's bam_prob_realn_core() and bam_cap_mapQ() have been moved
to HTSlib (with slightly altered names).
- - - - -
0c961b23 by Charles Plessy at 2016-04-26T20:39:39+09:00
Merge tag '1.3.1' into debian/unstable
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 (#432, #523, #529, #535, PR #530).
* All samtools commands now check for I/O errors more carefully, especially
when writing output files (#111, #253, #470, PR #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 (#532).
* The fastq -O option no longer crashes on reads that do not have an OQ tag
field (#517).
* The merge and sort commands now handle (unusual) BAM files that have no
textual @SQ headers (#548, #550).
* Sorting files containing @CO headers no longer duplicates the comment
headers, which previously happened on large sorts for which temporary
files were needed (#563).
* The rmdup and view -l commands no longer crash on @RG headers that do not
have a LB field (#538).
* Fixed miscellaneous issues #128, #130, #131, #489, and #514.
- - - - -
0de58f79 by Charles Plessy at 2016-04-26T20:42:02+09:00
New upstream release; no new copyright nor license notice.
- - - - -
3666b08e by Charles Plessy at 2016-04-26T20:57:11+09:00
Conforms with Policy version 3.9.8.
- - - - -
82c3bfa5 by Charles Plessy at 2016-04-26T20:58:18+09:00
Remove legacy statement on the libbam.
- - - - -
60c45b7e by Charles Plessy at 2016-04-26T21:12:25+09:00
samtools (1.3.1-1) unstable; urgency=medium
0c961b2 Merge tag '1.3.1' into debian/unstable
3666b08 Conforms with Policy version 3.9.8.
-- Charles Plessy <plessy at debian.org> Tue, 26 Apr 2016 21:12:05 +0900
- - - - -
f846d657 by John Marshall at 2016-04-26T13:27:54+01:00
Use HTSlib's new probaln_glocal() function
Samtools's kpa_glocal() has been moved to HTSlib (with a slightly
altered name).
- - - - -
4f9a3274 by John Marshall at 2016-04-26T15:29:00+01:00
Use HTSlib's new errmod_cal()/probaln_glocal()/sam_prob_realn() functions
Requires samtools/htslib at b183ab2d5abbff4592074b3ba177d84e550a7e3b (PR samtools/htslib#343).
Our errmod.[ch] conflicts with that added to HTSlib, so must be removed to
work with samtools/htslib at 55b2ae462619538b27cf64f518b03f4b56bb421a or later.
- - - - -
952da102 by Charles Plessy at 2016-04-27T10:02:02+09:00
Needs htslib 1.3.1.
Closes: #822701
- - - - -
02963988 by Charles Plessy at 2016-04-27T10:03:06+09:00
Current changelog.
- - - - -
9e4093d2 by John Marshall at 2016-05-06T15:09:48+01:00
Explicitly set @CURSES_LIB@ for --without-curses
If for some reason AX_WITH_CURSES is not expanded, autoconf will
never see CURSES_LIB/etc marked as output variables and not expand
@CURSES_LIB@/etc. As AX_WITH_CURSES is within a conditional, this is
particularly confusing for --without-curses. Fixes #528, but alters
nothing in normal circumstances.
(Set CURSES_LIB/etc to empty separately rather than with
AC_SUBST([CURSES_LIB], []), as with the latter the new code is
expanded to "else fi", which is a shell syntax error.)
- - - - -
a98b89bb by Charles Plessy at 2016-05-08T21:11:34+09:00
samtools (1.3.1-2) unstable; urgency=medium
952da10 Build-depends on htslib 1.3.1. (Closes: #822701)
-- Charles Plessy <plessy at debian.org> Sun, 08 May 2016 21:11:12 +0900
- - - - -
026c8d7f by John Marshall at 2016-05-10T14:11:47+01:00
Write BQ SAM line the same way as for AF
Avoid puts(NULL) and only clear kstring_t if write_cns is true.
Detected via GCC 6 -Wmisleading-indentation warning.
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e4446b5a by John Marshall at 2016-05-11T11:03:41+01:00
Use bcf_hdr_format() rather than deprecated bcf_hdr_fmt_text()
Uses new HTSlib function added in samtools/htslib at f581de8b6714cf69416ce6f9d4d4f050996699b8.
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e5dfb0aa by Rob Davies at 2016-05-13T15:03:01+01:00
Add samtools view tests for extracting unmapped reads.
Add test to make samtools view search for region '*', i.e. unmapped reads.
Add an extra reference (ref3_unused) to view.001.sam, view.001.fa and
view.001.fa.fai. This reference is the last in the header, but is not
used in the body of the file.
Detects the (htslib) bug described in issue samtools#568 (samtools
index/view bug with unmapped reads).
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1c1c2196 by James Bonfield at 2016-05-17T14:44:56+01:00
Fixed the out by one error in --insert-size.
Fixes #345.
(Changes proof-read by @daviesrob)
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b4e452c3 by James Bonfield at 2016-05-17T16:57:09+01:00
Added mpileup -a and -aa options
Fixes #496. Also fixed the tests for c1#pad1.bam and c1#pad2.bam;
they should have been known failures instead of know passes (see
issues samtools/htslib#57 and samtools/htslib#59).
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69567c8a by Martin Pollard at 2016-05-18T10:41:25+01:00
bam2fq_mainloop should be using filter_it_out
Remove duplicated code bam2fq_mainloop should be using filter_it_out rather than it's own copy of those lines.
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402aa76d by Matthieu Foll at 2016-05-18T16:54:40+02:00
Fixed the `-a` option for zero coverage positions
Fixes https://github.com/samtools/samtools/issues/374 after my [comment](https://github.com/samtools/samtools/issues/374#issuecomment-219427442)
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4dbadcfd by Rob Davies at 2016-05-19T12:27:28+01:00
Enforce a minimum memory requirement for samtools sort
Prevent accidents where sort creates one temporary file per input read
by refusing to run unless the -m parameter is set to at least 1 MiB.
If it doesn't run, it prints an error message explaining in detail why
not.
Includes a note in the man page describing the limit.
[NEWS]
* 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.
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4db01dd8 by James Bonfield at 2016-05-19T16:53:04+01:00
Improved error reporting in samtools index.
Along with the same named htslib branch, this fixes samtools#312.
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b2b81b4d by John Marshall at 2016-05-20T15:10:34+01:00
Merge sort memory requirement diagnostic (PR #581)
(Unindented the string text to improve 80-column legibility of the
source code.)
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4f8adc8f by John Marshall at 2016-05-20T15:15:22+01:00
Add NEWS item about mpileup zero coverage '*' fixes
Mention the output changes due to b4e452c3a0703d401b0e388b9b646e7495f13456
(see PR #537); they're surely minor, but it turns out they've been noticed:
https://sourceforge.net/p/samtools/mailman/message/35102141/ (samtools-help,
"Question relating to samtools mpileup output", 2016-05-19).
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d0c09f35 by Martin O. Pollard at 2016-05-23T14:01:35+01:00
Convert quickcheck to hts_check_EOF API to check EOF on CRAM
Convert quickcheck to hts_check_EOF API to check EOF on CRAM files and
avoid using BGZF internal APIs.
Add tests for samtools generated cram 3.0 and 2.1 (previous truncated
file was generated using scramble).
Make EOF check work on non-sequence data.
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44290ddc by James Bonfield at 2016-05-25T14:21:17+01:00
Depth/Mpileup -a fixes. Fixes #374.
These work with and without regions (-r). With bed files it's more
challenging. They mostly work, but the distinction between -a and -aa
is blurred and bed regions that are entirely absent of data may be
omitted even with the -aa option.
It is possible to fix this, but it will need surgery on the bed
parsing code which these changes don't touch. (Bed processing is
currently a completely opaque data structure with a minimal API.)
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9c5fd981 by James Bonfield at 2016-05-25T14:22:47+01:00
Added 30ish new tests for depth/mpileup -a and -aa.
Fixes samtools#374
Note that there is one case for each that is listed as a known
failure. If we use -a with a BED file and the BED file specifies a
region which has zero coverage, but that reference has coverage
elsewhere (and we are not using -r to filter out that region), then
the output will still include zero data for the BED region.
Thus in this scenario -a is acting as -aa should. Fixing this is
tricky, but probably there is little desire to use BED with the
inbetween -a (rather than -aa or no 'all' option).
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1395f125 by John Marshall at 2016-05-25T15:59:33+01:00
Fix Rob and Martin's whitespace [minor]
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675bff76 by John Marshall at 2016-05-25T16:06:58+01:00
Merge mpileup/depth -a/-aa fixes (PR #579, PR #586)
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2fa144fa by James Bonfield at 2016-05-25T17:19:10+01:00
Further depth/mpileup tests. Also improved documentation.
Sorry I somehow lost these in a stash while juggling something else
and didn't spot they got missed off the PR. (Already Travis checked on
my fork, but subsequently pushed directly as PR has been merged
already with modified history.)
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f458b7cc by John Marshall at 2016-05-26T11:29:57+01:00
Testclean and ignore test temporary files
Now ignores/cleans xx#depth*.bam*, so beware trying to add such files.
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39c4b673 by David K Jackson at 2016-06-01T15:44:22+01:00
Amend info regarding bedcov subcommand
Correct help message from command to note the -Q INT optional filter
works on mapping quality (not base quality). Report help messages
from depth and bedcov more consistently. Add -Q option to bedcov
entry in man page.
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cbea0f9e by John Marshall at 2016-06-02T10:37:12+01:00
Allow finer control over program vs. script installation
Use $(INSTALL_SCRIPT) to install scripts and $(INSTALL_MAN) to install
man pages. Install misc/* programs and scripts to $(misc_bindir),
which is $(bindir) by default but may be overridden.
TODO perhaps add a --with-misc-bindir configure option.
Now that $(MISC_SCRIPTS) is so named, remove BUILT_ from other variable
names so they parallel $(PROGRAMS).
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73c4054a by John Marshall at 2016-06-02T11:45:03+01:00
Add libst.a so test suite can use print_error()/etc
Move print_error()/print_error_errno() to a new sam_utils.c so
that test programs can use them without getting samtools's main().
Build a new libst.a (but DON'T add it to "lib" or "install" targets,
as it's for internal use here in samtools only) linked against by
both samtools and the test programs, as this sort of shared code
is likely to increase.
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29cfd701 by John Marshall at 2016-06-02T16:22:01+01:00
Use print_error/_errno() in bam_sort.c and bam_split.c
Followup to 24d3235d5ce920592a9f17ee947d5b72749b0eb6 now that these
are available to test programs.
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a04a7dda by John Marshall at 2016-06-02T16:39:43+01:00
Avoid printing "error message: Success" [minor]
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324d6621 by jenniferliddle at 2016-06-13T11:33:35+01:00
bam_split now adds @PG header to bam files (PR #557)
[Use a fixed string version of samtools_version() in test/test.c so
that tests can embed the constant in expected output; similiarly with
test_filter_header_rg.c's stringify_argv() usage. Fix memory leaks.
Update makefile dependencies. -- JM]
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f3178b74 by John Marshall at 2016-06-13T17:14:25+01:00
Avoid strndup() and strsep() for portability reasons
strndup() is in POSIX but unavailable on e.g. OS X < 10.7;
strsep() is not a POSIX function.
No need to duplicate the input in confirm_rg() or get_first_rgid() as they
don't modify it, and the header has come from bam_hdr_dup() so hdr->text
is always NUL-terminated.
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91283dd2 by John Marshall at 2016-06-21T15:58:16+01:00
In read_file_list(), check for URL syntax or extant files
Since 4b0058f506960786fc4c988c512cd462e02f24ed, read_file_list() checks
that the list file actually contains a plausible list of filenames (rather
than e.g. being itself a BAM file). We can't really check that remote URLs
actually exist, so check for valid URI scheme text or an extant local file.
Fixes #592.
TODO Potentially rewrite to use hts_readlist() instead.
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b25695bc by Anton Kratz at 2016-06-21T16:46:22+01:00
Add plot-bamstats -l / --log-y option
Added command line parameter parsing and Gnuplot code to plot the Y axis
of the Insert Size plot optionally in log10 scale.
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26e1ea5b by David K Jackson at 2016-06-27T13:52:20+01:00
Clarify bedcov subcommand usage
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de10fa3e by Rob Davies at 2016-07-18T13:36:45+01:00
Make samtools faidx write faster and detect write errors.
Replace the putchar() loop in faidx with a call to fwrite. With glibc
the reduction in function call overhead gives a roughly 70% speed increase.
Add checks for write failure, so faidx is more likely to notice if
something goes wrong. Also try to avoid a possible overflow if seq_len
is greater than INT_MAX - 60.
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613501f5 by John Marshall at 2016-07-18T15:18:52+01:00
Exterminate error(), fix memory leaks in event of write errors
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d1039b95 by John Marshall at 2016-08-03T11:03:18+01:00
Fix language misidentification of test data [minor]
Linguist was identifying test/dat/mpileup.*.[1-9] as groff (man page)
source due to their extensions, inflating the language statistics
shown on the GitHub repository.
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9df63211 by John Marshall at 2016-08-22T16:04:33+01:00
Use print_error_errno() to report file open failures
Further followup to 24d3235d5ce920592a9f17ee947d5b72749b0eb6;
report errno when reporting errors from hts_open() et al (cf #51).
In cut_target.c, print an error message instead of segfaulting.
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a9054c75 by Petr Danecek at 2016-10-07T10:12:09+01:00
Place percent mapped bases output in the correct field
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04ce2bcc by John Marshall at 2016-10-10T12:45:15+01:00
Improve view -s documentation
If you subsample repeatedly with the same seed value, you end up
subsampling to min(fractions) rather than to product(fractions) as you
would hope if the sampling was independent.
The use of srand()/rand() is really a red herring: we're not seeding the
random number generator to get a sequence of random numbers; rather we're
just using srand()/rand() once to ensure subsam_seed has several bits set
even when the user provides humane settings like 0, 1, 2, etc.
Overloading the -s value to set the seed remains obtuse; cf #217.
Documentation resolves #617 and similar mistakes.
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9aac9cbe by Sascha Steinbiss at 2016-10-20T20:03:25+00:00
fix FTBFS
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ce4a601a by John Marshall at 2016-10-21T13:57:05+01:00
Skip usage tests when pseudo-terminal can't be opened
Put `new IO::Pty` inside the eval too, so that we just skip these
tests in the unlikely event this fails, rather than aborting.
(Further to #300; cf @satta's part of https://bugs.debian.org/840974)
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db8bac6a by Sascha Steinbiss at 2016-10-23T13:35:15+00:00
use John Marshall's patch to address test pty issue
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90a26350 by Sascha Steinbiss at 2016-10-23T13:35:15+00:00
fall back to working ax_with_curses.m4
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070aa3e4 by Sascha Steinbiss at 2016-10-23T13:36:03+00:00
adjust d/changelog
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4dae08be by Sascha Steinbiss at 2016-10-24T16:33:37+02:00
dch -r
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0a150351 by Kevin Murray at 2016-11-04T12:08:13+00:00
Fix usage description of bamshuf/collate
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4b8bdd4a by John Marshall at 2017-01-05T14:08:54+00:00
Happy New Year
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1bae2510 by John Marshall at 2017-01-09T11:29:31+00:00
Listen to -o FILE option in samtools view -c
Also act on the -o option in is_count mode. Possibly we should use
hopen() instead so arbitrary URLs can be used, but for one %d being
output it seems like fopen() should suffice. Fixes #626.
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2b8f06d7 by Anton Khodak at 2017-01-12T00:30:46-08:00
Add CWL tools to the package
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12928834 by Anton Khodak at 2017-01-13T06:30:52-08:00
Add CWL tools
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11b2ae71 by Anton Khodak at 2017-01-14T09:01:44-08:00
minor fixes
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861db421 by Andreas Tille at 2017-01-15T10:00:32+01:00
Please use UNRELEASED as long as a package is not uploaded
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0bc88cab by Andreas Tille at 2017-01-15T10:02:15+01:00
Remove wrong debian-changes patch
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30bc5e2d by John Marshall at 2017-01-17T09:12:15+00:00
Add the autoconf macros required to the repository
Previously to build from a Git repository developers had to use aclocal
to get these macros from the Autoconf Archive (but release tarballs have
contained an already-built configure script, and will continue to).
This has been a source of user error, and since the following patches
http://git.savannah.gnu.org/cgit/autoconf-archive.git/commit/?id=6dc6cc55a1f3248c8bc39b0abcd5aeb4a3e34a06
http://git.savannah.gnu.org/cgit/autoconf-archive.git/commit/?id=0351b066631215b4fdc3c672a8ef90b233687655
the upstream version of AX_WITH_CURSES barely works and its interface
has been changed (see Debian bug 840974 <https://bugs.debian.org/840974>
comment #35 for details).
Hence we now include copies of autoconf-archive/m4/ax_with_curses.m4 as
at f7dd9928d94cdc780fea4fe17da03f9ccea24891 (serial 15) and serial 1 of
ax_with_htslib.m4 within this repository. It is not ideal to duplicate
external source code within the repository, but they change slowly and
this is now the lesser of two evils.
As an externally-provided ax_with_curses.m4 (in particular) does not
suffice, we've used plain autoconf m4_include rather than an aclocal
approach. (See <https://autotools.io/autoconf/macros.html>.)
README.md recommends `autoconf -Wno-syntax` in order to suppress the
"AC_CONFIG_SUBDIRS: you should use literals" warning. Autoreconf can
also be used, but emits this warning several times.
Fixes #500.
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28a611d2 by James Bonfield at 2017-01-26T12:40:49+00:00
Added multi-threaded decoding to view, index and sort.
These are copied from PR #595 and amalgamated into one commit.
The more contentious parts of that PR or ones not entirely related to
threading have been ditched.
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24971add by James Bonfield at 2017-02-09T15:01:20+00:00
Improved multi-threading support for many more samtools commands.
Now BAM has the ability to multi-thread the decoder, and the BAM
encoder threading is more efficient, many sub-commands can now
benefit. For those that already have multi-threading, these have also
migrated to using the sam_opts global option mechanism. (That's still
not an ideal interface, but it suffices for now.)
Sub-commands that have gained -@ or --threads, along with an estimated
speed up from single to 16 threads are:
calmd 5.6
fixmate 12.4
addreplacerg 11.8
collate 1.8
merge 5.0
sort 6.3 (1.4x faster than old 16-way threading)
fastq 1.7
fasta 2.2
view (readonly) 7.8 ("view -f 0xffff" to test decode only)
view (r/w) 12.6 (1.6x faster than old 16-way threading)
flagstat 8.2
index 7.2
split 12.5
Some are still far from ideal as they spend too long in the main
thread doing computation and very little doing decompression and
compression of BAMs. Sub-commands that I didn't try to change or did
but reverted as there is no significant speed benefit include
bedcov, depth, phase, depad, mpileup, targetcut and rmdup along with
various non BAM/CRAM related functions.
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002eb0aa by Rob Davies at 2017-02-10T16:17:25+00:00
Remove redundant item from long options array
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3a7d0f02 by Rob Davies at 2017-02-10T16:41:39+00:00
Update some tests to run both single and multi-threaded
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2e84f7b1 by Martin O. Pollard at 2017-02-13T13:41:53+00:00
Add MC support to fixmates
Add mate cigar tag support to fixmate and fix tests. (Fixes #170)
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9adfa139 by Martin O. Pollard at 2017-02-13T13:51:03+00:00
Add error handling to kstring functions in bam_mate
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e5f5ba1a by Martin O. Pollard at 2017-02-13T14:04:42+00:00
Fixmates: add tests for two reads unmapped
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d02c177e by Rob Davies at 2017-02-14T10:25:47+00:00
Temporarily disable the large_chrom bai index test
It doesn't work properly, and gets in the way of fixing the problem
in htslib.
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c39caa47 by James Bonfield at 2017-02-20T14:57:41+00:00
Replaced bool with int to avoid confusion with true being failure.
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80ed7c79 by James Bonfield at 2017-02-20T16:42:43+00:00
Merged PR#545 (Add MC support to fixmates)
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6c4929d2 by James Bonfield at 2017-02-20T16:43:53+00:00
Fix to 28a611d2 to prevent samtools view crash on error handling.
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90b0baa5 by Shane McCarthy at 2017-02-23T17:15:01+00:00
index: update error message for failure to index
After samtools/htslib#470, which fixes the underlying issue #241,
we update the error message upon failure to index. See
https://github.com/samtools/samtools/issues/241#issuecomment-279783955
Closes #241
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cbee45e4 by steveb-cirina at 2017-02-24T13:34:51-08:00
Fixed a typo: changed "suffices" to "suffixes".
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6587a2b1 by Rob Davies at 2017-03-02T09:08:01+00:00
Use htslib_static.mk to get static link flags
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5ec72f17 by James Bonfield at 2017-03-02T12:21:13+00:00
Mention multi-threaded BAM/CRAM decoding.
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979bac9b by James Bonfield at 2017-03-06T13:41:32+00:00
Merge branch PR #649 (Use htslib_static.mk to get static link flags)
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1bf9afa0 by jenniferliddle at 2017-03-06T16:27:11+00:00
Updated with 1.4 changes
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c63b06e0 by Rob Davies at 2017-03-09T16:49:27+00:00
Add liblzma and libbz2 to travis.
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3f0407f1 by Rob Davies at 2017-03-09T21:49:29+00:00
Stop samtools configure from always trying to configure htslib
Add an option --enable-configure-htslib to allow configuration of htslib
to be turned on and off. The default is to only configure htslib when
it is in a subdirectory of samtools (as happens with the distribution
tarballs), and only if --with-htslib=search is used.
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e5838c2c by Rob Davies at 2017-03-13T10:37:21+00:00
Update INSTALL with new library dependencies
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0a859b10 by jenniferliddle at 2017-03-13T14:48:47+00:00
Release 1.4: summary
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a230f81a by jenniferliddle at 2017-03-13T14:54:16+00:00
Merge version number bump and NEWS file from master
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bda1d8ab by Andreas Tille at 2017-03-21T16:23:40+01:00
Merge tag '1.4' into debian/unstable
Release 1.4 (13 March 2017)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Noteworthy changes in samtools:
* Fixed Issue #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 (#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 #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 (#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 #589; thanks to Anton Kratz).
* Fixmate will now also add and update MC (mate CIGAR) tags.
- - - - -
f83cd5e8 by Andreas Tille at 2017-03-21T16:26:52+01:00
Replaced Dominique Belhachemi by my own ID as Uploader
- - - - -
0dafb696 by Andreas Tille at 2017-03-21T16:29:23+01:00
Adapt patches
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7e76eb3f by Andreas Tille at 2017-03-21T19:16:55+01:00
Bump versioned Depends: libhts-dev (>= 1.4), upload to experimental
- - - - -
32563cce by Andreas Tille at 2017-03-21T21:43:13+01:00
Rebuild against properly named libhts which had a soname change
- - - - -
f5120bef by awenger at 2017-03-22T14:27:05+00:00
Add "-b <bam.fofn>" flag to samtools cat.
Add a "-b <bam.fofn>" like that in "samtools merge" to "samtools cat".
This alleviates any problems with the list of input file name exceeding
the number of characters permitted in a single command.
[jkb during merge: adjusted memory freeing and usage format.]
- - - - -
ea2cbba5 by James Bonfield at 2017-03-22T14:38:42+00:00
Document the "-b bam-list" option to samtools cat.
- - - - -
ea171c4d by James Bonfield at 2017-03-22T15:09:08+00:00
Remove two tiny memory leaks in samtools merge.
- - - - -
692e0583 by James Bonfield at 2017-03-23T11:43:35+00:00
Cram lossy names (#543)
* Added missing input/output options to the man page.
* Rewording of input/output options.
Given the command line options are --input-fmt-options and
--output-fmt-options, it seemed wiser to use the phrases "CRAM input
only" and "CRAM output only" when documenting the input/output option
strings. It still refers to encoding and decoding elsewhere, but I
think this is sufficiently clear.
- - - - -
86dddab2 by Jennifer Liddle at 2017-03-27T16:49:27+01:00
Merge pull request #560 from george-hall-wtsi/tab_completion
Implemented tab completion
- - - - -
90b995fd by Rob Davies at 2017-03-28T15:02:37+01:00
Merge pull request to enable large vertical movement in tview (#257)
Includes trivial update to replace tabs with spaces.
- - - - -
8c20354d by Blaise Li at 2017-03-29T10:10:46+01:00
Option -G to exclude based on a set of bits.
I wanted to be able to exclude reads having a given combination of bits set in
the SAM flag. For instance, to exclude reads where both mates are unmapped, use
`samtools view -G 12`
Did I miss how to do it with -f and -F ?
(Committer: jkb - fixed bam2fq bug to handle -G0 correctly.)
- - - - -
b1b6717e by James Bonfield at 2017-03-30T17:33:24+01:00
Improved wording of usage and updated man page.
- - - - -
8b779df3 by James Bonfield at 2017-03-31T09:49:09+01:00
Another change to view/bam2fq filtering wording.
The previous attempt had "unset" in the wrong place possibly, but it's
now been reworded in terms of flags instead of bits (potentially
permitting the symbolic flag characters again in the future).
- - - - -
11295209 by James Bonfield at 2017-04-07T09:15:04+01:00
Improvements for C99/XOPEN compliance.
Replaced alloca with malloc.
Avoid arithmetic on void*.
Ensure unsigned types for bit fields.
Use of strings.h for strcasecmp.
- - - - -
64852009 by James Bonfield at 2017-04-07T09:15:23+01:00
Switch to -lpthread instead of -pthread for linking.
See https://github.com/samtools/htslib/pull/255 for analogous htslib change.
- - - - -
6d612fea by jenniferliddle at 2017-04-21T14:35:14+01:00
Added option to produce fastq files from BC or other tags
jkb: Removed xstr() and ifmt strdup.
- - - - -
d7b0234d by James Bonfield at 2017-04-21T16:57:45+01:00
Output CRAM as temporary sort format iff there are more than 64k cigar ops.
Fixes #667.
In theory we could use CRAM for all temporary output files, but
currently it is too high in memory usage. See the comments included
in this commit for a discussion on how this could be avoided, but for
now we are making the smallest change that fixes the issue as there
are larger issues yet to resolve in sort memory usage.
- - - - -
0aa9fab9 by James Bonfield at 2017-04-24T09:27:25+01:00
Bam2fq comment improvements (no code changed).
- - - - -
f13cf4af by James Bonfield at 2017-05-08T10:47:53+01:00
NEWS update.
(Ideally merge on day on release, editing date if required.)
- - - - -
8f8600a1 by jenniferliddle at 2017-05-08T11:07:57+01:00
Release 1.4.1: summary
- - - - -
2ba4095f by Andreas Tille at 2017-06-18T21:04:10+02:00
Merge tag '1.4.1' into debian/unstable
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. (#560)
* Samtools tview now has J and K keys for verticale movement by 20
lines. (#257)
* Various compilation / portability improvements.
* Fixed issue with more than 65536 CIGAR operations and SAM/CRAM files.
(#667)
- - - - -
dd7a1172 by Andreas Tille at 2017-06-18T21:07:39+02:00
New upstream version
- - - - -
ae321344 by Andreas Tille at 2017-06-18T21:12:00+02:00
Close bug, upload to unstable
- - - - -
8a06c510 by Andreas Tille at 2017-07-20T12:14:20+02:00
New upstream version 1.5
- - - - -
5eef3584 by Andreas Tille at 2017-07-20T12:14:22+02:00
Updated version 1.5 from '1.5'
with Debian dir 1f9b98601b18347e19cc5281a1b3b962281ce872
- - - - -
1655d1e2 by Andreas Tille at 2017-07-20T12:15:04+02:00
New upstream version
- - - - -
30920881 by Andreas Tille at 2017-07-20T12:16:28+02:00
debhelper 10
- - - - -
d52cd132 by Andreas Tille at 2017-07-20T12:17:05+02:00
Standards-Version: 4.0.0 (no changes needed)
- - - - -
3c0ec5c1 by Andreas Tille at 2017-07-20T12:18:15+02:00
Bump versioned Build-Depends: libhts-dev (>= 1.5)
- - - - -
d3b61134 by Andreas Tille at 2017-08-04T17:58:02+02:00
Add recommends to cwl-tool and fix shebang line of cwl scripts
- - - - -
7f525ad6 by Andreas Tille at 2017-08-04T18:55:59+02:00
Do not warn about cwl-runner , upload to unstable
- - - - -
2b7a1c63 by Steffen Moeller at 2017-09-10T11:33:20+02:00
Added references to registries
- - - - -
007dfe06 by Andreas Tille at 2017-12-11T15:18:42+01:00
Switch to default Debian Med repository layout
- - - - -
8abd6926 by Andreas Tille at 2017-12-11T15:18:48+01:00
New upstream version 1.6
- - - - -
eec880f9 by Andreas Tille at 2017-12-11T15:19:04+01:00
Update upstream source from tag 'upstream/1.6'
Update to upstream version '1.6'
with Debian dir 290d6313b34baaaab2f22325cf86f755d204ed21
- - - - -
9e3a866a by Andreas Tille at 2017-12-11T15:26:51+01:00
Drop literal_version.patch since upstream does not use make to obtain version number any more
- - - - -
4eb68d19 by Andreas Tille at 2017-12-11T15:27:22+01:00
Update patches.
- - - - -
6ec08ddc by Andreas Tille at 2017-12-11T15:29:04+01:00
Remove deactivated patch
- - - - -
9a27c5cd by Andreas Tille at 2017-12-11T15:29:38+01:00
Standards-Version: 4.1.2
- - - - -
18c5fa05 by Andreas Tille at 2017-12-11T15:34:23+01:00
Remove unused lintian-overrides
- - - - -
938dd3f4 by Andreas Tille at 2017-12-11T15:55:01+01:00
Upload to experimental
- - - - -
f41c6b34 by Andreas Tille at 2017-12-11T16:21:27+01:00
Forwarded patch to upstream
- - - - -
815e6da0 by Andreas Tille at 2017-12-13T07:44:43+01:00
Fix versioned Build-Depends
- - - - -
7649e519 by Andreas Tille at 2017-12-13T08:06:47+01:00
Comment that this was applied upstream
- - - - -
f722e30b by Andreas Tille at 2017-12-14T16:10:28+01:00
Upload to unstable
- - - - -
931933e0 by Graham Inggs at 2017-12-23T09:05:16+02:00
Reduce per-thread memory limit of sort tests, upload to unstable
- - - - -
d3c6ed11 by Andreas Tille at 2018-02-14T09:50:25+01:00
New upstream version 1.7
- - - - -
e27e46fb by Andreas Tille at 2018-02-14T09:50:51+01:00
Update upstream source from tag 'upstream/1.7'
Update to upstream version '1.7'
with Debian dir fe1426d99a1e800c51b64f733eaa53a2119e1b2b
- - - - -
77f81d66 by Andreas Tille at 2018-02-14T09:51:12+01:00
New upstream version
- - - - -
fffda22f by Andreas Tille at 2018-02-14T09:51:42+01:00
Standards-Version: 4.1.3
- - - - -
8fde52ae by Andreas Tille at 2018-02-14T10:00:06+01:00
TODO: Adpapt patches
- - - - -
619dfea0 by Andreas Tille at 2018-02-14T13:21:56+01:00
adapted patches, mahem patch was applied upstream
- - - - -
0ac413af by Andreas Tille at 2018-02-14T13:23:38+01:00
Bump versioned Build-Depends: libhts-dev (>= 1.7), upload to unstable
- - - - -
526f3eee by Steffen Möller at 2018-03-28T11:23:48+00:00
Updated bio.tools RRID in d/u/metadata
- - - - -
f2b1311a by Andreas Tille at 2018-03-29T10:00:01+02:00
Install examples (since it is used in dwgsim package and might be helpful for users in general)
- - - - -
d639c077 by Andreas Tille at 2018-03-29T10:00:01+02:00
debhelper 11
- - - - -
a91d8b33 by Andreas Tille at 2018-03-29T10:00:01+02:00
Upload to unstable
- - - - -
d8af890c by Andreas Tille at 2018-03-29T10:01:41+02:00
Remove outdated information
- - - - -
0fddc947 by Andreas Tille at 2018-04-09T14:35:16+02:00
Remove invalid fields from debian/upstream/metadata
- - - - -
1452aced by Andreas Tille at 2018-05-03T12:02:04+02:00
New upstream version 1.8
- - - - -
cf330a23 by Andreas Tille at 2018-05-03T12:02:20+02:00
Update upstream source from tag 'upstream/1.8'
Update to upstream version '1.8'
with Debian dir c1791e4b4b846627ac181c5e25a26f548469b133
- - - - -
2cb67ab6 by Andreas Tille at 2018-05-03T12:02:20+02:00
New upstream version
- - - - -
0ccaa5ae by Andreas Tille at 2018-05-03T12:02:23+02:00
Point Vcs fields to salsa.debian.org
- - - - -
cb2185b4 by Andreas Tille at 2018-05-03T12:02:24+02:00
Standards-Version: 4.1.4
- - - - -
5ff7c75e by Andreas Tille at 2018-05-03T13:08:38+02:00
Update patches
- - - - -
e5d95bc9 by Andreas Tille at 2018-05-03T13:15:14+02:00
hardening=+all
- - - - -
e2e77e3d by Andreas Tille at 2018-05-03T13:16:19+02:00
Bump versioned Build-Depends: libhts-dev (>= 1.8)
- - - - -
1c37793d by Andreas Tille at 2018-05-03T13:21:28+02:00
Upload to experimental
- - - - -
7f2247a0 by Charles Plessy at 2018-05-11T09:44:04+09:00
Mention the CRAM format in the description.
- - - - -
7ad3cb16 by Steffen Möller at 2018-05-11T10:20:12+00:00
Updated RRID->SciCrunch in d/u/metadata
- - - - -
fc3ddb2b by Andreas Tille at 2018-09-10T21:34:16+02:00
New upstream version 1.9
- - - - -
c36ba43a by Andreas Tille at 2018-09-10T21:34:33+02:00
Update upstream source from tag 'upstream/1.9'
Update to upstream version '1.9'
with Debian dir 0b13529ef06d0e309f1ddc937c1d412a67d688f7
- - - - -
d1a74f64 by Andreas Tille at 2018-09-10T22:12:11+02:00
New upstream version
- - - - -
fb68a4b1 by Andreas Tille at 2018-09-10T22:12:49+02:00
Fix Perl interpreter line
- - - - -
dd9e4966 by Andreas Tille at 2018-09-10T22:14:57+02:00
Standards-Version: 4.2.1
- - - - -
1ce8831f by Andreas Tille at 2018-09-12T21:48:14+02:00
Upload to unstable
- - - - -
ede04b46 by Michael R. Crusoe at 2019-01-03T00:21:12-08:00
Turn on SSE for i386.
- - - - -
ccfdd9ac by Andreas Tille at 2019-02-04T08:06:33+01:00
Do not force sse for i386
- - - - -
6457c973 by Andreas Tille at 2019-02-04T08:06:59+01:00
debhelper 12
- - - - -
5063d6b0 by Andreas Tille at 2019-02-04T08:08:28+01:00
Respect DEB_BUILD_OPTIONS in override_dh_auto_test target
- - - - -
c965dae8 by Andreas Tille at 2019-02-04T08:13:11+01:00
Upload to unstable
- - - - -
44703ca0 by Michael R. Crusoe at 2019-02-04T00:19:11-08:00
Mark samtools-test as Multi-Arch: foreign.
- - - - -
770284c7 by Andreas Tille at 2019-02-21T15:34:06+01:00
Update debian/README.Debian
- - - - -
a49f55a4 by Andreas Tille at 2019-02-21T15:41:21+01:00
Drop reduntant information in debian/reference. It is maintained in debian/upstream/metadata now
- - - - -
ec29cbbe by Andreas Tille at 2019-02-21T15:42:24+01:00
Drop invalid comment - we are using canonical layout of git-buildpackage now
- - - - -
9587f1d1 by Andreas Tille at 2019-02-21T15:59:16+01:00
install upstream NEWS as upstream changelog
- - - - -
3c46ee23 by Andreas Tille at 2019-02-21T16:03:11+01:00
install upstream README as doc
- - - - -
d1997a02 by Andreas Tille at 2019-02-21T17:45:18+01:00
more complete debian/NEWS.Debian
- - - - -
d7024e0e by Andreas Tille at 2019-02-21T17:55:59+01:00
Upload to unstable
- - - - -
26784c71 by Andreas Tille at 2019-03-16T18:28:18+01:00
Use <!nocheck> for libio-pty-perl
- - - - -
73c7856e by Michael R. Crusoe at 2019-08-17T10:19:43+02:00
drop any-i386
- - - - -
16a6a5be by Michael R. Crusoe at 2019-08-17T10:20:02+02:00
debhelper-compat 12
- - - - -
ce17a6c7 by Michael R. Crusoe at 2019-08-17T10:20:05+02:00
Standards-Version: 4.4.0
- - - - -
71066ba6 by Michael R. Crusoe at 2019-08-17T10:21:00+02:00
release to unstable
- - - - -
5b1c474a by Steffen Möller at 2019-10-17T16:35:05+00:00
Update metadata with ref to conda
- - - - -
0b80afbb by Andreas Tille at 2019-12-03T11:45:22+01:00
Port Python2 script to Python3 using 2to3
- - - - -
30c29179 by Andreas Tille at 2019-12-03T11:45:41+01:00
Standards-Version: 4.4.1
- - - - -
909aa9ba by Andreas Tille at 2019-12-03T11:45:44+01:00
Set fields Upstream-Name in debian/copyright.
- - - - -
8bf7ff1d by Andreas Tille at 2019-12-03T11:45:44+01:00
Set upstream metadata fields: Repository-Browse.
- - - - -
82f11d9c by Andreas Tille at 2019-12-03T11:45:45+01:00
Remove obsolete fields Name from debian/upstream/metadata.
- - - - -
0a09a539 by Andreas Tille at 2019-12-03T11:50:48+01:00
Use python3 dependency once the script was converted
- - - - -
49f62d75 by Andreas Tille at 2019-12-03T11:55:41+01:00
Upload to unstable
- - - - -
e3705033 by Michael R. Crusoe at 2019-12-11T11:01:22+01:00
Resume building on any as htslib has regained any-i386
- - - - -
8dac8123 by Michael R. Crusoe at 2019-12-11T11:53:06+01:00
New upstream version 1.10
- - - - -
5118a544 by Michael R. Crusoe at 2019-12-11T11:53:32+01:00
Update upstream source from tag 'upstream/1.10'
Update to upstream version '1.10'
with Debian dir 82cf39c264dd38e3886be253e11153d597eaaec4
- - - - -
556aaa66 by Michael R. Crusoe at 2019-12-11T11:55:32+01:00
1.10-1
- - - - -
3ae5e220 by Michael R. Crusoe at 2019-12-11T11:55:37+01:00
freshen patches
- - - - -
18118746 by Michael R. Crusoe at 2019-12-11T11:57:52+01:00
more build deps
- - - - -
76214378 by Michael R. Crusoe at 2019-12-16T16:14:17+01:00
new test path
- - - - -
d10c1db9 by Michael R. Crusoe at 2019-12-16T16:17:34+01:00
1.10-1
- - - - -
48bdcecf by Michael R. Crusoe at 2019-12-25T14:55:26+01:00
1.10-2: breaks older iva and bio-tradis
- - - - -
02eb5b73 by Michael R. Crusoe at 2019-12-25T17:16:00+01:00
Allow tests to fail on mipsel due to lack of memory
- - - - -
e8c62ffa by Andreas Tille at 2020-06-09T11:28:41+02:00
cwltools only "Suggests" not "Recommends"
- - - - -
81ac71e9 by Andreas Tille at 2020-06-09T11:38:41+02:00
There are no Python scripts provided in samtools any more
- - - - -
95afd029 by Andreas Tille at 2020-06-18T22:52:29+02:00
Close bug
- - - - -
0e522cb4 by Andreas Tille at 2020-06-19T11:41:02+02:00
routine-update: Standards-Version: 4.5.0
- - - - -
58200bd8 by Andreas Tille at 2020-06-19T11:41:02+02:00
routine-update: debhelper-compat 13
- - - - -
55bc2fb6 by Andreas Tille at 2020-06-19T11:41:20+02:00
routine-update: Add salsa-ci file
- - - - -
ed0a6251 by Andreas Tille at 2020-06-19T11:41:20+02:00
routine-update: Rules-Requires-Root: no
- - - - -
2077b332 by Andreas Tille at 2020-06-19T11:41:39+02:00
Set upstream metadata fields: Bug-Database, Bug-Submit, Repository.
Fixes: lintian: upstream-metadata-missing-bug-tracking
See-also: https://lintian.debian.org/tags/upstream-metadata-missing-bug-tracking.html
- - - - -
a0e76b08 by Andreas Tille at 2020-06-19T11:41:40+02:00
Replace use of deprecated $ADTTMP with $AUTOPKGTEST_TMP.
Fixes: lintian: uses-deprecated-adttmp
See-also: https://lintian.debian.org/tags/uses-deprecated-adttmp.html
- - - - -
ae79f578 by Andreas Tille at 2020-06-19T11:50:04+02:00
routine-update: Ready to upload to unstable
- - - - -
97559533 by Andreas Tille at 2020-10-01T15:54:29+02:00
routine-update: New upstream version
- - - - -
eaf4eea9 by Andreas Tille at 2020-10-01T15:54:30+02:00
New upstream version 1.11
- - - - -
99fb4783 by Andreas Tille at 2020-10-01T15:54:52+02:00
Update upstream source from tag 'upstream/1.11'
Update to upstream version '1.11'
with Debian dir 69670b13b9a616812f79f8edb27ef10387e05d13
- - - - -
be2dde94 by Andreas Tille at 2020-10-01T15:56:33+02:00
Drop spelling patch
- - - - -
0ca30e00 by Andreas Tille at 2020-10-01T16:04:34+02:00
Versioned Build-Depends: libhts-dev (>= 1.11)
- - - - -
cc518eba by Andreas Tille at 2020-10-01T16:09:46+02:00
TODO: Clarify autopkgtest error
- - - - -
12b93bb4 by Andreas Tille at 2020-10-01T16:46:02+02:00
Upload to unstable
- - - - -
a7be9a5e by Steffen Möller at 2021-03-06T19:42:50+00:00
Update metadata - added ref to guix
- - - - -
65ce8d20 by Étienne Mollier at 2021-08-27T16:09:51+02:00
routine-update: New upstream version
- - - - -
81e41a8b by Étienne Mollier at 2021-08-27T16:09:52+02:00
New upstream version 1.13
- - - - -
b807b948 by Étienne Mollier at 2021-08-27T16:10:18+02:00
Update upstream source from tag 'upstream/1.13'
Update to upstream version '1.13'
with Debian dir 8a88a12b17a0c6914a92a8b6e80a87a5bb19fbce
- - - - -
43491b32 by Étienne Mollier at 2021-08-27T16:10:18+02:00
routine-update: Standards-Version: 4.6.0
- - - - -
56b04e55 by Étienne Mollier at 2021-08-27T16:10:22+02:00
Use secure URI in Homepage field.
Changes-By: lintian-brush
Fixes: lintian: homepage-field-uses-insecure-uri
See-also: https://lintian.debian.org/tags/homepage-field-uses-insecure-uri.html
- - - - -
fd8c7614 by Étienne Mollier at 2021-08-27T16:10:25+02:00
routine-update: watch file standard 4
- - - - -
5c77b324 by Étienne Mollier at 2021-08-27T16:13:44+02:00
routine-update: Ready to upload to unstable
- - - - -
11e7fc5f by Étienne Mollier at 2021-08-27T16:17:29+02:00
d/control: add myself to uploaders
- - - - -
85e377ee by Étienne Mollier at 2021-08-27T19:13:30+02:00
d/control: bump B-D libhts-dev (>= 1.13~)
Attempts to build samtools against older versions are bound to fail,
and will prevent migration to testing of the lot. Thanks Nilesh for
the tip!
- - - - -
d05af603 by Étienne Mollier at 2021-08-27T19:16:41+02:00
update changelog
- - - - -
c95b66e8 by Andreas Tille at 2021-08-30T16:32:13+02:00
make the build reproducible
- - - - -
fc228655 by Andreas Tille at 2021-08-30T16:34:55+02:00
routine-update: Ready to upload to unstable
- - - - -
ee4c97ec by Étienne Mollier at 2021-10-24T19:24:53+02:00
d/rules: fix several issues in manual pages
Most of these were reported by lintian as bad-whatis-entry or
groff-message. Some are still under the radar though.
- - - - -
488881b3 by Étienne Mollier at 2021-10-24T19:29:15+02:00
Add fix-ftbfs-mvprintw.patch
Closes: #997180
- - - - -
d9a87518 by Étienne Mollier at 2021-10-24T19:35:17+02:00
d/rules: prudent pattern to fix whatis entries
Gbp-Dcp: ignore
- - - - -
da4dc4ae by Étienne Mollier at 2021-10-24T19:50:10+02:00
d/rules: disable executable bit on ac_test.bed
- - - - -
fbfd6c99 by Étienne Mollier at 2021-10-24T19:52:33+02:00
Add samtools-fasta-q-whatis.patch
- - - - -
06566462 by Étienne Mollier at 2021-10-24T19:56:34+02:00
update changelog
- - - - -
4cfbf2b4 by Étienne Mollier at 2021-10-24T20:00:08+02:00
d/samtools.lintian-overrides removed *.py pattern
Apparently, the samtools do not ship python scripts anymore.
- - - - -
015d4162 by Étienne Mollier at 2021-10-24T20:28:55+02:00
Adjust fix-ftbfs-mvprintw.patch metainformations
Thanks: John Marshall
This is done in the light of information forwarded upstream and
existing patch with minimum change.
- - - - -
a35323b7 by Étienne Mollier at 2021-10-24T20:31:11+02:00
ready to upload to unstable
- - - - -
650b7a7f by Étienne Mollier at 2021-10-25T00:17:24+02:00
d/rules: only disable executable bit if test package is built.
- - - - -
9c337903 by Étienne Mollier at 2021-10-25T00:18:53+02:00
update changelog
- - - - -
7a4e09b0 by Étienne Mollier at 2021-10-25T20:53:12+02:00
ready for upload to unstable, and close bug
- - - - -
d9595e92 by Andreas Tille at 2021-12-07T08:57:22+01:00
routine-update: New upstream version
- - - - -
b14cda59 by Andreas Tille at 2021-12-07T08:57:23+01:00
New upstream version 1.14
- - - - -
691f3aa0 by Andreas Tille at 2021-12-07T08:57:41+01:00
Update upstream source from tag 'upstream/1.14'
Update to upstream version '1.14'
with Debian dir 59157f3e7e626bcb67af25eeae86b0c476b7abb6
- - - - -
b929904f by Andreas Tille at 2021-12-07T09:12:21+01:00
Cleanup Breaks/Replaces
- - - - -
aedf2068 by Andreas Tille at 2021-12-07T09:12:29+01:00
Refresh patches
- - - - -
46030bbf by Andreas Tille at 2021-12-07T14:56:30+01:00
Upload to experimental
- - - - -
f91c2417 by Andreas Tille at 2021-12-08T13:20:13+01:00
Upload to experimental
- - - - -
af8a82dd by Andreas Tille at 2022-09-30T11:34:14+02:00
routine-update: New upstream version
- - - - -
8be6d9fc by Andreas Tille at 2022-09-30T11:34:14+02:00
New upstream version 1.16.1
- - - - -
bdfbb004 by Andreas Tille at 2022-09-30T11:34:34+02:00
Update upstream source from tag 'upstream/1.16.1'
Update to upstream version '1.16.1'
with Debian dir d207ba1f50984d231dfc00fafac4dd2623aeec48
- - - - -
1964346e by Andreas Tille at 2022-09-30T11:34:34+02:00
routine-update: Standards-Version: 4.6.1
- - - - -
0cb20ea2 by Andreas Tille at 2022-09-30T11:45:49+02:00
Refresh patches
- - - - -
e051fd0f by Andreas Tille at 2022-09-30T11:48:56+02:00
Upload to unstable
- - - - -
f92998e4 by Étienne Mollier at 2023-06-12T20:34:13+02:00
routine-update: New upstream version
- - - - -
16dda270 by Étienne Mollier at 2023-06-12T20:34:14+02:00
New upstream version 1.17
- - - - -
e038e722 by Étienne Mollier at 2023-06-12T20:34:30+02:00
Update upstream source from tag 'upstream/1.17'
Update to upstream version '1.17'
with Debian dir 7083a0de4b9ae81e7003016619b5c4804d76e36c
- - - - -
99aa7c6b by Étienne Mollier at 2023-06-12T20:34:30+02:00
routine-update: Standards-Version: 4.6.2
- - - - -
aebe148f by Étienne Mollier at 2023-06-12T20:37:00+02:00
samtools-fasta-q-whatis.patch: unfuzz
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dac74908 by Étienne Mollier at 2023-06-12T20:37:15+02:00
d/control: clean obsolete package from Breaks:
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5d5421ae by Étienne Mollier at 2023-06-12T20:38:38+02:00
update changelog
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66a6b6e0 by Étienne Mollier at 2023-06-12T20:53:14+02:00
d/control: build depends on libhts-dev (>= 1.17~)
Trying to build against older versions will result at best with:
reset.c:107:20: warning: implicit declaration of function ‘bam_aux_first’; did you mean ‘bam_aux_get’? [-Wimplicit-function-declaration]
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f3e3ea1a by Étienne Mollier at 2023-06-12T20:54:37+02:00
d/control: build depends on libncurses-dev
This replaces the build dependency on libncurses5-dev, which is
flagged as obsolete by lintian.
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7adec786 by Étienne Mollier at 2023-06-12T20:59:35+02:00
d/*.lintian-overrides: update mismatched override
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1cc8cf98 by Étienne Mollier at 2023-06-12T23:27:59+02:00
update changelog
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dddb318e by Étienne Mollier at 2023-06-18T23:25:58+02:00
typos.patch: new patch.
This fixes various typos caught by a few of the lintian parsers.
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0fd429ba by Étienne Mollier at 2023-06-18T23:28:06+02:00
ready to upload to experimental.
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1efadf4b by Étienne Mollier at 2023-06-22T22:33:14+02:00
ready to migrate to unstable.
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e756607e by Étienne Mollier at 2023-07-12T21:43:52+02:00
typos.patch: forwarded upstream.
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4d39be10 by Étienne Mollier at 2023-07-12T21:51:46+02:00
samtools-fasta-q-whatis.patch: forwarded upstream.
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fd467500 by Andreas Tille at 2023-11-08T07:21:22+01:00
routine-update: New upstream version
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3e070ffd by Andreas Tille at 2023-11-08T07:21:23+01:00
New upstream version 1.18
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c1b903d9 by Andreas Tille at 2023-11-08T07:21:41+01:00
Update upstream source from tag 'upstream/1.18'
Update to upstream version '1.18'
with Debian dir 3484f1d7031e63311a715859da209fd1a4a7e30a
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71817c1d by Andreas Tille at 2023-11-08T07:26:58+01:00
Remove patches applied upstream
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0a4b8fb8 by Andreas Tille at 2023-11-08T09:05:52+01:00
Autopkgtest is now using run-unit-test as user example
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8c8f2a28 by Andreas Tille at 2023-11-08T09:09:34+01:00
Upload to unstable
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58f62524 by Étienne Mollier at 2023-12-15T16:06:55+01:00
routine-update: New upstream version
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73082b5f by Étienne Mollier at 2023-12-15T16:06:55+01:00
New upstream version 1.19
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73e62d8d by Étienne Mollier at 2023-12-15T16:07:12+01:00
Update upstream source from tag 'upstream/1.19'
Update to upstream version '1.19'
with Debian dir b967cbff08ac44966a6bd23088b8ca45d645757c
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b86781db by Étienne Mollier at 2023-12-15T16:11:51+01:00
d/rules: adjust dh_instalchangelogs.
Upstream NEWS file has been renamed NEWS.md.
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66fa6ba6 by Étienne Mollier at 2023-12-15T17:36:45+01:00
ready to upload to unstable.
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4ce4e038 by Étienne Mollier at 2024-02-17T18:08:13+01:00
routine-update: New upstream version
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3f34445e by Étienne Mollier at 2024-02-17T18:08:14+01:00
New upstream version 1.19.2
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13ea07af by Étienne Mollier at 2024-02-17T18:08:28+01:00
Update upstream source from tag 'upstream/1.19.2'
Update to upstream version '1.19.2'
with Debian dir b891069a499ebe09ea58013b0b6694776a592328
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e0d4f37f by Étienne Mollier at 2024-02-17T18:21:44+01:00
d/control: replace pkg-config by pkgconf.
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915b7e32 by Étienne Mollier at 2024-02-17T18:22:54+01:00
ready to upload to unstable.
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6733c3c2 by Étienne Mollier at 2024-05-29T15:03:06+02:00
New upstream version 1.20
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90a09619 by Étienne Mollier at 2024-05-29T15:03:22+02:00
Update upstream source from tag 'upstream/1.20'
Update to upstream version '1.20'
with Debian dir 0c9a8b0c00a6fb58bf78642dea0d042b83beebf6
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2b57a203 by Étienne Mollier at 2024-05-29T15:04:50+02:00
d/copyright: update copyright year.
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4f1b2424 by Étienne Mollier at 2024-05-29T15:05:28+02:00
d/control: declare compliance to standards version 4.7.0.
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922ea172 by Étienne Mollier at 2024-05-29T15:13:39+02:00
d/rules: fix permissions of a data file in samtools-test.
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5c53e568 by Étienne Mollier at 2024-05-29T15:14:22+02:00
ready for upload to unstable.
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832f44a8 by Étienne Mollier at 2024-05-30T20:02:35+02:00
d/control: build depends on libhts-dev >= 1.20~.
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c2e7702d by Étienne Mollier at 2024-05-30T20:51:20+02:00
this upload ended up accepted into unstable.
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56a4a288 by Étienne Mollier at 2024-05-30T20:51:47+02:00
d/rules: fix no-arch-all builds.
The initial issue flown below radar due to leftover htslib version
discrepancy.
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c449bd74 by Étienne Mollier at 2024-05-30T20:53:35+02:00
ready to upload to unstable.
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4d88bb51 by Michael R. Crusoe at 2024-11-14T12:34:54+01:00
New upstream version 1.21
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604c7739 by Michael R. Crusoe at 2024-11-14T12:34:54+01:00
New upstream version
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70892c0f by Michael R. Crusoe at 2024-11-14T12:35:14+01:00
Update upstream source from tag 'upstream/1.21'
Update to upstream version '1.21'
with Debian dir 56313df8ab2a8964f030941dba216a7a5beb6dd6
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afec6610 by Michael R. Crusoe at 2024-11-14T17:56:28+01:00
d/rules: build-depend on newer htslib 1.21
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7dc80624 by Michael R. Crusoe at 2024-11-14T17:56:28+01:00
routine-update: Ready to upload to experimental
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8 changed files:
- − .gitattributes
- − .gitignore
- − .travis.yml
- INSTALL
- LICENSE
- Makefile
- − Makefile.mingw
- − NEWS
The diff was not included because it is too large.
View it on GitLab: https://salsa.debian.org/med-team/samtools/-/compare/9be38118d45c2819cc672043f9b9be8ed771a9bd...7dc806249b0af0853a95d6c7629e18a04a39c469
--
View it on GitLab: https://salsa.debian.org/med-team/samtools/-/compare/9be38118d45c2819cc672043f9b9be8ed771a9bd...7dc806249b0af0853a95d6c7629e18a04a39c469
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