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samtools.git
2010-11-02
Heng Li
Separate kaln and kprobaln as I am preparing further...
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2010-11-02
Petr Danecek
Added -b option: read file names from a file
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2010-10-30
Heng Li
* samtools-0.1.9-2 (r787)
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2010-10-29
Heng Li
* samtools-0.1.9-1 (r786)
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2010-10-29
Heng Li
Optionally output "DP", the individual read depth
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2010-10-28
Heng Li
acknowledge Petr and John who have greatly contributed...
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2010-10-28
Heng Li
Release samtools-0.1.9 (r783)
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2010-10-27
Heng Li
fixed a silly bug in pileup
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2010-10-27
Heng Li
* samtools-0.1.8-22 (r781)
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2010-10-27
Heng Li
* samtools-0.1.8-21 (r780)
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2010-10-27
Heng Li
improve pileup a little bit
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2010-10-27
Heng Li
* samtools-0.1.8-20 (r778)
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2010-10-26
Heng Li
* samtools-0.1.8-19 (r777)
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2010-10-26
Heng Li
remove local realignment (probabilistic realignment...
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2010-10-21
On behalf of...
Add the relevant filename or region to error messages...
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2010-10-19
Heng Li
* Minor code changes. No real effect.
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2010-10-19
Heng Li
added another toy example
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2010-10-14
Heng Li
improve the LD statistics
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2010-10-13
Heng Li
* a minor fix to the -L option
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2010-10-12
Heng Li
a minor change
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2010-10-12
Heng Li
forget to add the key file
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2010-10-12
Heng Li
* vcfutils.pl: fixed a typo in help message
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2010-10-11
Heng Li
added filter for samtools/bcftools genetated VCFs
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2010-10-05
Heng Li
* removed a comment line in kaln.c
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2010-10-05
Petr Danecek
Convert VCF output of "bcftools view -bgcv" to a valid...
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2010-10-03
Heng Li
* samtools-0.1.8-18 (r763)
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2010-10-03
Heng Li
* vcfutils.pl qstats: calculate marginal ts/tv
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2010-10-01
Heng Li
I am changing the gap open probability back to 0.001...
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2010-10-01
Heng Li
* samtools-0.1.8-17 (r760)
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2010-09-30
Heng Li
mark samtools-0.1.8-16 (r759)
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2010-09-30
Heng Li
round to the nearest integer
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2010-09-28
Heng Li
I was trying to accelerate ka_prob_glocal() as this...
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2010-09-28
Heng Li
this is interesting. multiplication is much faster...
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2010-09-28
Heng Li
minor changes
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2010-09-28
Heng Li
prob_realn() seems working!
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2010-09-28
Heng Li
minor
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2010-09-28
Heng Li
Convert phredQ to probabilities
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2010-09-28
Heng Li
Implement the glocal HMM; discard the extention HMM
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2010-09-28
Heng Li
improve numerical stability
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2010-09-28
Heng Li
more comments
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2010-09-28
Heng Li
fixed a bug in banded DP
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2010-09-28
Heng Li
* fixed that weird issue.
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2010-09-28
Heng Li
More comments. This version seems working, but somethin...
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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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