[med-svn] samtools annotated tag 0.1.9 created (now b009d87)
Charles Plessy
plessy at moszumanska.debian.org
Tue Dec 10 10:06:31 UTC 2013
This is an automated email from the git hooks/post-receive script.
plessy pushed a change to annotated tag 0.1.9
in repository samtools.
at b009d87 (tag)
tagging ac32543c12eac42f12e0c66b78c3d53211caeaab (commit)
replaces 0.1.8
tagged by On behalf of Heng Li
on Thu Oct 28 03:51:59 2010 +0100
- Log -----------------------------------------------------------------
Samtools 0.1.9, including ChangeLog.old and win32/lib*.a files
that were missing from the canonical release tarball, but without
the samtools.txt file (generated from samtools.1) that is found
in the tarball.
Heng Li (132):
* samtools-0.1.8-1 (r615)
* added mutli-sample framework. It is not working, yet.
* samtools-0.1.8-2 (r617)
* preliminary multisample SNP caller.
* samtools-0.1.8-3 (r627)
calculate posterior allele frequency
added an alternative prior
added the format column
another minor fix to mpileup
posterior expectation FINALLY working. I am so tired...
minor tweaks
minor changes
* samtools-0.1.8-6 (r638)
* samtools-0.1.8-7 (r639)
NOT ready yet. Going to make further changes...
supposedly this is THE correct implementation, but more testing is needed
* fixed a STUPID bug, which cost me a lot of time.
* samtools-0.1.8-8 (r644)
Generate binary VCF
* samtools-0.1.8-9 (r649)
fixed a bug
fixed a bug in bcf reader
fixed a memory leak
missing a column in VCF output...
* fixed a bug
* samtools-0.1.8-10 (r658)
fixed another minor bug
move bcftools to samtools
fixed compilation error
added more examples
spec
* allow to set min base q
* added prelimiary VCF parser (not finished)
unfinished vcf parser
minor
* the code base is stablized again.
* samtools-0.1.8-11 (r672)
Fisher's exact test
* Special functions: log(gamma()), erfc(), P(a,x) (incomplete gamma)
* bcftools: add HWE (no testing for now)
reimplement incomplete gamma functions. no copy-paste
* test depth, end distance and HWE
perform single-tail test for ED4
help messages
* improved kstring (added kstrtok)
* fixed a bug in kstrtok at kstring.c
* parse PL
do not print refname if file is converted from VCF
fixed an issue in parsing integer
* a numerically stable method to calculate z_{jk}
faster for large sample size (in principle)
use float for QUAL
* write a little more VCF header
allow to read the prior from the error output. EM iteration is working.
added revised MAQ error model
* use the revised MAQ error model for mpileup
remove VCF output in mpileup
* samtools-0.1.8-12 (r692)
print QUAL as floating numbers
change the default correlation coefficient
added regularized incomplete beta function
* samtools-0.1.8-13 (r698)
fixed a bug in calculating the t statistics
* rename vcfout.c as call1.c
z' and z'' can be calculated
preliminary contrast variant caller
Utilities for processing VCF
more commands for my own uses
Write the correct ALT and PL in the SNP calling mode.
Do not compile _BCF_QUAD by default
* fixed bugs in parsing VCF
fixed another problem
SNP calling from the GL field
* changed 3.434 to 4.343 (typo!)
quite a lot changes to the contrast caller, but I still feel something is missing...
* samtools-0.1.8-13 (r715)
* aggressive gapped aligner is implemented in calmd.
minor changes. It is BUGGY now!
fixed a bug in realignment
fixed a minor issue
fixed a bug in realignment
dynamic band width in realignment
* convert BCF to QCALL input
* added varFilter to vcfutils.pl
* samtools-0.1.8-14 (r727)
* fixed a bug in razip: -c will delete the input file
* fixed a bug in capQ
fixed a bug in indexing
* put n_smpl to "bcf1_t" to simplify API a little
* added comments
hapmap2vcf convertor
convert UCSC SNP SQL dump to VCF
improve qstats by checking the alleles as well
* merge files region-by-region. work on small examples but more tests are needed.
* samtools-0.1.8-15 (r379)
...
A little code cleanup. Now the forward and backback algorithms give
More comments. This version seems working, but something is a little weird...
* fixed that weird issue.
fixed a bug in banded DP
more comments
improve numerical stability
Implement the glocal HMM; discard the extention HMM
Convert phredQ to probabilities
minor
prob_realn() seems working!
minor changes
this is interesting. multiplication is much faster than division, at least on my Mac
I was trying to accelerate ka_prob_glocal() as this will be the
round to the nearest integer
mark samtools-0.1.8-16 (r759)
* samtools-0.1.8-17 (r760)
I am changing the gap open probability back to 0.001. It seems that
* vcfutils.pl qstats: calculate marginal ts/tv
* samtools-0.1.8-18 (r763)
* removed a comment line in kaln.c
added filter for samtools/bcftools genetated VCFs
* vcfutils.pl: fixed a typo in help message
forget to add the key file
a minor change
* a minor fix to the -L option
improve the LD statistics
added another toy example
* Minor code changes. No real effect.
remove local realignment (probabilistic realignment is still there)
* samtools-0.1.8-19 (r777)
* samtools-0.1.8-20 (r778)
improve pileup a little bit
* samtools-0.1.8-21 (r780)
* samtools-0.1.8-22 (r781)
fixed a silly bug in pileup
Release samtools-0.1.9 (r783)
On behalf of John Marshall (8):
Add svn:ignore properties listing the generated files.
Add svn:ignore properties for generated files that don't appear in "make all".
0 is a successful return value from bam_read1(). (In practice, it never
When bam_read1() returns an error (return value <= -2), propagate that error
Add bam_validate1().
Use bam_validate1() to detect garbage records in the event of a corrupt
Abort if merge -h's INH.SAM cannot be opened, just as we abort
Add the relevant filename or region to error messages, and cause a failure
Petr Danecek (1):
Convert VCF output of "bcftools view -bgcv" to a valid VCF file
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