2010-12-02 |
Heng Li | a possible fix to DP4=0,0,0,0; have not tested, but... |
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2010-12-02 |
Heng Li | * samtools-0.1.11-1 (r858) |
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2010-11-26 |
Heng Li | * fixed a memory violation |
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2010-11-23 |
Heng Li | fixed a typo/bug in r^2 computation |
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2010-11-22 |
Heng Li | Release samtools-0.1.11 |
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2010-11-20 |
Heng Li | * samtools-0.1.10-9 (r844) |
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2010-11-18 |
Heng Li | * modify the filtering rule: also filter SNPs around... |
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2010-11-16 |
Heng Li | bcftools: allow to skip indels |
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2010-11-16 |
Heng Li | * samtools-0.1.9-17 (r824) |
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2010-11-15 |
Heng Li | * samtools-0.1.9-16 (r822) |
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2010-11-12 |
Heng Li | * samtools-0.1.19-11 (r817) |
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2010-11-10 |
Heng Li | fixed a typo |
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2010-11-10 |
Heng Li | use zlib for direct reading when BCF_LITE is in use |
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2010-11-10 |
Heng Li | * samtools-0.1.9-8 (r807) |
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2010-11-10 |
Heng Li | bcftools: compute equal-tail (Bayesian) credible interval |
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2010-11-09 |
Heng Li | added a double-hit filter to avoid overestimated indel... |
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2010-11-09 |
Heng Li | * samtools-0.1.9-6 (r803) |
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2010-11-08 |
Heng Li | fixed another silly bug in mpileup's indel caller |
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2010-11-03 |
Heng Li | fixed a minor problem in the example coming with kprobaln.c |
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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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2010-10-14 |
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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2010-09-20 |
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 | * 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 | fixed a minor issue |
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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 | print QUAL as floating numbers |
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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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2010-08-05 |
Heng Li | * the code base is stablized again. |
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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 | fixed compilation error |
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2010-08-04 |
Heng Li | move bcftools to samtools |
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