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samtools.git
2010-08-31
Heng Li
z' and z'' can be calculated
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2010-08-31
Heng Li
* rename vcfout.c as call1.c
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2010-08-24
Heng Li
fixed a bug in calculating the t statistics
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2010-08-24
Heng Li
* samtools-0.1.8-13 (r698)
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2010-08-24
Heng Li
added regularized incomplete beta function
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2010-08-23
Heng Li
change the default correlation coefficient
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2010-08-23
Heng Li
print QUAL as floating numbers
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2010-08-23
Heng Li
* samtools-0.1.8-12 (r692)
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2010-08-23
Heng Li
remove VCF output in mpileup
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2010-08-23
Heng Li
* use the revised MAQ error model for mpileup
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2010-08-20
Heng Li
added revised MAQ error model
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2010-08-18
Heng Li
allow to read the prior from the error output. EM itera...
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2010-08-17
Heng Li
* write a little more VCF header
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2010-08-17
Heng Li
use float for QUAL
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2010-08-14
Heng Li
faster for large sample size (in principle)
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2010-08-14
Heng Li
* a numerically stable method to calculate z_{jk}
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2010-08-12
Heng Li
fixed an issue in parsing integer
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2010-08-09
Heng Li
do not print refname if file is converted from VCF
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2010-08-09
Heng Li
* parse PL
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2010-08-09
Heng Li
* fixed a bug in kstrtok@kstring.c
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2010-08-09
Heng Li
* improved kstring (added kstrtok)
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2010-08-09
Heng Li
help messages
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2010-08-09
Heng Li
perform single-tail test for ED4
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2010-08-09
Heng Li
* test depth, end distance and HWE
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2010-08-08
Heng Li
reimplement incomplete gamma functions. no copy-paste
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2010-08-07
Heng Li
* bcftools: add HWE (no testing for now)
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2010-08-06
Heng Li
* Special functions: log(gamma()), erfc(), P(a,x)...
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2010-08-06
Heng Li
Fisher's exact test
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2010-08-06
Heng Li
* samtools-0.1.8-11 (r672)
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2010-08-05
Heng Li
* the code base is stablized again.
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2010-08-05
Heng Li
minor
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2010-08-05
Heng Li
unfinished vcf parser
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2010-08-05
Heng Li
* added prelimiary VCF parser (not finished)
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2010-08-04
Heng Li
* allow to set min base q
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2010-08-04
Heng Li
spec
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2010-08-04
Heng Li
added more examples
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2010-08-04
Heng Li
fixed compilation error
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2010-08-04
Heng Li
move bcftools to samtools
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2010-08-03
Heng Li
fixed another minor bug
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2010-08-03
Heng Li
* samtools-0.1.8-10 (r658)
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2010-08-03
Heng Li
* fixed a bug
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2010-08-02
Heng Li
missing a column in VCF output...
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2010-08-02
Heng Li
fixed a memory leak
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2010-08-02
Heng Li
fixed a bug in bcf reader
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2010-08-02
Heng Li
fixed a bug
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2010-08-02
Heng Li
* samtools-0.1.8-9 (r649)
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2010-08-02
Heng Li
Generate binary VCF
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2010-07-28
Heng Li
* samtools-0.1.8-8 (r644)
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2010-07-28
Heng Li
* fixed a STUPID bug, which cost me a lot of time.
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2010-07-28
Heng Li
supposedly this is THE correct implementation, but...
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2010-07-28
Heng Li
NOT ready yet. Going to make further changes...
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2010-07-26
Heng Li
* samtools-0.1.8-7 (r639)
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2010-07-25
Heng Li
* samtools-0.1.8-6 (r638)
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2010-07-24
Heng Li
minor changes
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2010-07-24
Heng Li
minor tweaks
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2010-07-24
Heng Li
posterior expectation FINALLY working. I am so tired...
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2010-07-23
Heng Li
another minor fix to mpileup
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2010-07-23
Heng Li
added the format column
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2010-07-23
Heng Li
added an alternative prior
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2010-07-23
Heng Li
calculate posterior allele frequency
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2010-07-23
Heng Li
* samtools-0.1.8-3 (r627)
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2010-07-22
Heng Li
* preliminary multisample SNP caller.
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2010-07-14
Heng Li
* samtools-0.1.8-2 (r617)
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2010-07-14
Heng Li
* added mutli-sample framework. It is not working...
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2010-07-13
Heng Li
* samtools-0.1.8-1 (r615)
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2010-07-12
Heng Li
Release samtools-0.1.8
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2010-07-12
Heng Li
fixed a compiling issue for Windows
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2010-07-12
Heng Li
fixed a bug in sorting when output to stdout (by Peter...
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2010-07-09
Heng Li
change the command line option of pileup
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2010-07-09
Heng Li
make pileup work with CIGAR with I/D at the beginning...
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2010-07-09
Heng Li
* make tview more friendly
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2010-07-08
Heng Li
* samtools-0.1.7-r607
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2010-07-08
Heng Li
removed a debugging example
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2010-07-08
Heng Li
* samtools-.1.7-18 (r605)
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2010-07-02
Heng Li
fixed a minor bug in idxstats
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2010-06-16
Heng Li
fixed a minor bug in indexing
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2010-06-15
Heng Li
change printf() to puts in exporting
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2010-06-14
Heng Li
minor fix. No actual effect.
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2010-06-14
Heng Li
added Makefile targets to compile shared/dynamic library
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2010-06-13
Heng Li
* samtools-0.1.7-17 (r596)
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2010-06-13
Heng Li
* samtools-0.1.7-16 (r595)
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2010-06-13
Heng Li
fixed a bug for unmapped sequences in indexing
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2010-06-12
Heng Li
rename iterf as iter
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2010-06-12
Heng Li
* samtools-0.1.7-15 (r592)
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2010-06-12
Heng Li
* samtools-0.1.7-14 (r591)
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2010-06-12
Heng Li
* samtools-0.1.7-13 (r590)
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2010-06-12
Heng Li
* samtools-0.1.7-12 (r589)
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2010-06-11
Heng Li
* samtools-0.1.7-11 (r588)
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2010-06-11
Heng Li
* samtools-0.1.7-10 (r587)
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2010-06-11
Heng Li
* samtools-0.1.7-9 (r586)
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2010-06-11
Heng Li
* samtools-0.1.7-8 (r585)
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2010-06-11
Heng Li
* samtools-0.1.7-7 (r584)
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2010-06-11
Petr Danecek
Initial release on behalf of Aylwyn Scally
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2010-05-07
Petr Danecek
Added a note about the indels coordinates
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2010-04-23
Petr Danecek
Added the possibility to print or not to print the...
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2010-04-15
Petr Danecek
More descriptive message for space separated tags
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2010-04-14
Petr Danecek
Speedup with -i, no need to query the reference all...
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2010-03-15
Petr Danecek
Fixed the order of sequences in the header
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2010-03-04
Petr Danecek
Added possibility to select indels only and fixed a...
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2010-02-27
On behalf of...
Improve the invalid 'BAM\1' magic number error message...
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