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samtools.git
2010-09-27
Heng Li
A little code cleanup. Now the forward and backback...
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2010-09-27
Heng Li
...
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2010-09-27
On behalf of...
Abort if merge -h's INH.SAM cannot be opened, just...
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2010-09-24
On behalf of...
Use bam_validate1() to detect garbage records in the...
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2010-09-24
On behalf of...
Add bam_validate1().
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2010-09-22
Heng Li
* samtools-0.1.8-15 (r379)
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2010-09-22
On behalf of...
When bam_read1() returns an error (return value <=...
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2010-09-22
On behalf of...
0 is a successful return value from bam_read1(). ...
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2010-09-20
Heng Li
* merge files region-by-region. work on small examples...
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2010-09-20
Heng Li
improve qstats by checking the alleles as well
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2010-09-17
Heng Li
convert UCSC SNP SQL dump to VCF
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2010-09-17
Heng Li
hapmap2vcf convertor
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2010-09-17
Heng Li
* added comments
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2010-09-17
Heng Li
* put n_smpl to "bcf1_t" to simplify API a little
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2010-09-17
Heng Li
fixed a bug in indexing
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2010-09-16
Heng Li
* fixed a bug in capQ
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2010-09-16
Heng Li
* fixed a bug in razip: -c will delete the input file
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2010-09-16
Heng Li
* samtools-0.1.8-14 (r727)
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2010-09-16
Heng Li
* added varFilter to vcfutils.pl
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2010-09-15
Heng Li
* convert BCF to QCALL input
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2010-09-15
Heng Li
dynamic band width in realignment
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2010-09-15
Heng Li
fixed a bug in realignment
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2010-09-15
Heng Li
fixed a minor issue
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2010-09-14
Heng Li
fixed a bug in realignment
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2010-09-14
Heng Li
minor changes. It is BUGGY now!
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2010-09-14
Heng Li
* aggressive gapped aligner is implemented in calmd.
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2010-09-14
On behalf of...
Add svn:ignore properties for generated files that...
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2010-09-13
On behalf of...
Add svn:ignore properties listing the generated files.
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2010-09-08
Heng Li
* samtools-0.1.8-13 (r715)
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2010-09-03
Heng Li
quite a lot changes to the contrast caller, but I still...
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2010-09-03
Heng Li
* changed 3.434 to 4.343 (typo!)
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2010-09-02
Heng Li
SNP calling from the GL field
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2010-09-01
Heng Li
fixed another problem
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2010-09-01
Heng Li
* fixed bugs in parsing VCF
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2010-09-01
Heng Li
Do not compile _BCF_QUAD by default
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2010-09-01
Heng Li
Write the correct ALT and PL in the SNP calling mode.
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2010-09-01
Heng Li
more commands for my own uses
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2010-09-01
Heng Li
Utilities for processing VCF
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2010-08-31
Heng Li
preliminary contrast variant caller
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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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