illumina/hap.py issues and pull requests

#100 - Merge content from internal repo for release

Pull Request - State: closed - Opened by dskola about 5 years ago

#100 - Merge content from internal repo for release

Pull Request - State: closed - Opened by dskola about 5 years ago

#99 - Option --no-rebuild-external doesn't exist

Issue - State: open - Opened by serge2016 about 5 years ago - 1 comment

#99 - Option --no-rebuild-external doesn't exist

Issue - State: open - Opened by serge2016 about 5 years ago - 1 comment

#98 - ERROR preprocess: vcf.c:3472: bcf_update_format: Assertion `!fmt->p_free' failed.

Issue - State: open - Opened by serge2016 about 5 years ago - 7 comments

#98 - ERROR preprocess: vcf.c:3472: bcf_update_format: Assertion `!fmt->p_free' failed.

Issue - State: open - Opened by serge2016 about 5 years ago - 7 comments

#97 - Add bin directory to PATH

Issue - State: open - Opened by serge2016 about 5 years ago

#97 - Add bin directory to PATH

Issue - State: open - Opened by serge2016 about 5 years ago

#96 - Java installation failuture

Issue - State: open - Opened by serge2016 about 5 years ago

#96 - Java installation failuture

Issue - State: open - Opened by serge2016 about 5 years ago

#95 - Post installation validation test fails

Issue - State: open - Opened by adigorla about 5 years ago - 6 comments

#95 - Post installation validation test fails

Issue - State: open - Opened by adigorla about 5 years ago - 6 comments

#94 - Target region specification: weird observation

Issue - State: open - Opened by ghost over 5 years ago

#94 - Target region specification: weird observation

Issue - State: open - Opened by ghost over 5 years ago

#93 - ERROR [stderr] Added region file '/tmp/tmpBkykHu.bed' as 'CONF'

Issue - State: open - Opened by 24natasya over 5 years ago

#93 - ERROR [stderr] Added region file '/tmp/tmpBkykHu.bed' as 'CONF'

Issue - State: open - Opened by 24natasya over 5 years ago

#92 - CalledProcessError: With Octopus VCF

Issue - State: open - Opened by 24natasya over 5 years ago - 6 comments

#92 - CalledProcessError: With Octopus VCF

Issue - State: open - Opened by 24natasya over 5 years ago - 6 comments

#91 - Definition of TS_boundary and TS_contained regions

Issue - State: open - Opened by ofonov over 5 years ago - 1 comment

#91 - Definition of TS_boundary and TS_contained regions

Issue - State: open - Opened by ofonov over 5 years ago - 1 comment

#90 - Another Hap.py installation error related to stdc++

Issue - State: open - Opened by peterlchang over 5 years ago - 1 comment

#90 - Another Hap.py installation error related to stdc++

Issue - State: open - Opened by peterlchang over 5 years ago - 1 comment

#89 - Fix an error in Variant decomposition test

Pull Request - State: closed - Opened by haodongchen over 5 years ago

#89 - Fix an error in Variant decomposition test

Pull Request - State: closed - Opened by haodongchen over 5 years ago

#88 - Question on Hap.py

Issue - State: open - Opened by elowy01 over 5 years ago

#88 - Question on Hap.py

Issue - State: open - Opened by elowy01 over 5 years ago

#87 - Inconsistent ROC reporting compared to labeled VCF

Issue - State: open - Opened by ksw9 over 5 years ago

#87 - Inconsistent ROC reporting compared to labeled VCF

Issue - State: open - Opened by ksw9 over 5 years ago

#86 - Warning in log file ("Too many AD fields") for gatk-vcf only

Issue - State: open - Opened by ghost over 5 years ago - 3 comments

#86 - Warning in log file ("Too many AD fields") for gatk-vcf only

Issue - State: open - Opened by ghost over 5 years ago - 3 comments

#85 - Docker

Issue - State: open - Opened by ktadler over 5 years ago - 1 comment

#85 - Docker

Issue - State: open - Opened by ktadler over 5 years ago - 1 comment

#84 - FP.al behavior at non-matching SNP alleles.

Issue - State: closed - Opened by jaredo over 5 years ago - 4 comments

#84 - FP.al behavior at non-matching SNP alleles.

Issue - State: closed - Opened by jaredo over 5 years ago - 4 comments

#83 - reference error

Issue - State: closed - Opened by ktadler over 5 years ago - 2 comments

#83 - reference error

Issue - State: closed - Opened by ktadler over 5 years ago - 2 comments

#82 - Fix with gcc 7.3

Pull Request - State: closed - Opened by pkrusche over 5 years ago - 2 comments

#82 - Fix with gcc 7.3

Pull Request - State: closed - Opened by pkrusche over 5 years ago - 2 comments

#81 - hap.py annotated VCF file as output issues running with docker

Issue - State: open - Opened by achimmiri over 5 years ago - 1 comment

#81 - hap.py annotated VCF file as output issues running with docker

Issue - State: open - Opened by achimmiri over 5 years ago - 1 comment

#80 - Parsimony

Issue - State: open - Opened by Jordi-V over 5 years ago - 3 comments

#80 - Parsimony

Issue - State: open - Opened by Jordi-V over 5 years ago - 3 comments

#79 - Is it possible to output 0/0 and ./. positions in VCF?

Issue - State: open - Opened by afzm over 5 years ago - 6 comments

#79 - Is it possible to output 0/0 and ./. positions in VCF?

Issue - State: open - Opened by afzm over 5 years ago - 6 comments

#78 - Truth and reference have no chromosomes in common

Issue - State: closed - Opened by litaifang over 5 years ago - 5 comments

#78 - Truth and reference have no chromosomes in common

Issue - State: closed - Opened by litaifang over 5 years ago - 5 comments

#77 - Inconsistent output for runs with and without stratification files

Issue - State: open - Opened by ofonov over 5 years ago

#77 - Inconsistent output for runs with and without stratification files

Issue - State: open - Opened by ofonov over 5 years ago

#76 - som.py script not working on examples

Issue - State: open - Opened by preetida almost 6 years ago - 2 comments

#76 - som.py script not working on examples

Issue - State: open - Opened by preetida almost 6 years ago - 2 comments

#75 - command quantify while running the below command

Issue - State: open - Opened by KrithikaSubramanian almost 6 years ago - 4 comments

#75 - command quantify while running the below command

Issue - State: open - Opened by KrithikaSubramanian almost 6 years ago - 4 comments

#74 - no genotype or ts/tv stratification

Issue - State: open - Opened by mikyatope almost 6 years ago - 1 comment

#74 - no genotype or ts/tv stratification

Issue - State: open - Opened by mikyatope almost 6 years ago - 1 comment

#73 - Variant in truth set outside confident region not marked UNK

Issue - State: closed - Opened by anands-repo almost 6 years ago - 1 comment

#73 - Variant in truth set outside confident region not marked UNK

Issue - State: closed - Opened by anands-repo almost 6 years ago - 1 comment

#72 - Hap.py not evaluating chromosomes in regions bed

Issue - State: open - Opened by ExpressionAnalysis almost 6 years ago

#72 - Hap.py not evaluating chromosomes in regions bed

Issue - State: open - Opened by ExpressionAnalysis almost 6 years ago

#71 - Inconsistent output when reversing truth and query

Issue - State: open - Opened by bjtrost almost 6 years ago - 2 comments

#71 - Inconsistent output when reversing truth and query

Issue - State: open - Opened by bjtrost almost 6 years ago - 2 comments

#70 - Question about possible mislabel of FN

Issue - State: closed - Opened by nh13 almost 6 years ago - 1 comment

#70 - Question about possible mislabel of FN

Issue - State: closed - Opened by nh13 almost 6 years ago - 1 comment

#69 - Update read me with GCC/G++ 4.9.2+ requirement

Pull Request - State: closed - Opened by nh13 almost 6 years ago - 1 comment

#69 - Update read me with GCC/G++ 4.9.2+ requirement

Pull Request - State: closed - Opened by nh13 almost 6 years ago - 1 comment

#68 - support for python3?

Issue - State: open - Opened by gopi1616 about 6 years ago

#68 - support for python3?

Issue - State: open - Opened by gopi1616 about 6 years ago

#67 - Deletion excluded due to padding base?

Issue - State: closed - Opened by andyb3 about 6 years ago - 2 comments

#66 - ERROR [stderr] regex_error

Issue - State: open - Opened by Xingsl about 6 years ago - 11 comments

#66 - ERROR [stderr] regex_error

Issue - State: open - Opened by Xingsl about 6 years ago - 11 comments

#65 - collect2: error: ld returned 1 exit status

Issue - State: open - Opened by lachlansimpson about 6 years ago - 2 comments

#64 - Python requirements: both 2.7 and 3.x or only 2.7?

Issue - State: closed - Opened by lachlansimpson about 6 years ago - 1 comment

#64 - Python requirements: both 2.7 and 3.x or only 2.7?

Issue - State: closed - Opened by lachlansimpson about 6 years ago - 1 comment

#63 - QQ field for ROC curves

Issue - State: open - Opened by rohandavidg about 6 years ago - 2 comments

#63 - QQ field for ROC curves

Issue - State: open - Opened by rohandavidg about 6 years ago - 2 comments

#62 - strelka2 variants error

Issue - State: open - Opened by sebastiandeorowicz about 6 years ago

#62 - strelka2 variants error

Issue - State: open - Opened by sebastiandeorowicz about 6 years ago

#61 - scmp-distance engine

Issue - State: open - Opened by virenar about 6 years ago - 1 comment

#61 - scmp-distance engine

Issue - State: open - Opened by virenar about 6 years ago - 1 comment

#60 - If `-o` is set to the same thing as the input VCF, hap.py will over-write the input

Issue - State: open - Opened by ifiddes-10x-zz over 6 years ago - 1 comment

#60 - If `-o` is set to the same thing as the input VCF, hap.py will over-write the input

Issue - State: open - Opened by ifiddes-10x-zz over 6 years ago - 1 comment

#59 - Reference header in output vcf hardcoded to HG19

Issue - State: open - Opened by kachulis over 6 years ago

#59 - Reference header in output vcf hardcoded to HG19

Issue - State: open - Opened by kachulis over 6 years ago

#58 - Clarify that INFO.VQSLOD is required for --roc

Pull Request - State: closed - Opened by EvanTheB over 6 years ago - 2 comments

#58 - Clarify that INFO.VQSLOD is required for --roc

Pull Request - State: closed - Opened by EvanTheB over 6 years ago - 2 comments

#57 - How to get a roc curve?

Issue - State: closed - Opened by EvanTheB over 6 years ago - 3 comments

#57 - How to get a roc curve?

Issue - State: closed - Opened by EvanTheB over 6 years ago - 3 comments

#56 - TRUTH.TP not equal to QUERY.TP for InDels

Issue - State: closed - Opened by wangguangya60 over 6 years ago - 1 comment

#56 - TRUTH.TP not equal to QUERY.TP for InDels

Issue - State: closed - Opened by wangguangya60 over 6 years ago - 1 comment

#55 - Is it possible to evaluate vcf of tetraploid species?

Issue - State: open - Opened by afzm over 6 years ago - 2 comments

#55 - Is it possible to evaluate vcf of tetraploid species?

Issue - State: open - Opened by afzm over 6 years ago - 2 comments

#54 - Input file has no samples. Hap.py will not like that.

Issue - State: closed - Opened by afzm over 6 years ago - 3 comments

#54 - Input file has no samples. Hap.py will not like that.

Issue - State: closed - Opened by afzm over 6 years ago - 3 comments

#53 - Very high memory usage in SGE

Issue - State: closed - Opened by wangguangya60 over 6 years ago - 3 comments

#53 - Very high memory usage in SGE

Issue - State: closed - Opened by wangguangya60 over 6 years ago - 3 comments

#52 - Incorrect variant position representation in error logs

Issue - State: closed - Opened by ManavalanG over 6 years ago - 3 comments

#52 - Incorrect variant position representation in error logs

Issue - State: closed - Opened by ManavalanG over 6 years ago - 3 comments

#51 - /bin/ld: cannot find -lstdc++ error

Issue - State: closed - Opened by gezthxbio over 6 years ago - 1 comment

#51 - /bin/ld: cannot find -lstdc++ error

Issue - State: closed - Opened by gezthxbio over 6 years ago - 1 comment

#50 - bcftools error

Issue - State: closed - Opened by jdoolittlehall over 6 years ago - 1 comment

#50 - bcftools error

Issue - State: closed - Opened by jdoolittlehall over 6 years ago - 1 comment

GitHub / illumina/hap.py issues and pull requests