From a75e1d4ce4f298a53aeef572202fa94a75380d9e Mon Sep 17 00:00:00 2001 From: Geraldine Van der Auwera Date: Tue, 17 Mar 2015 04:26:03 -0400 Subject: [PATCH] Fixes the test that was failing due to gsalib build failure --- .../src/R/R/gsa.reshape.concordance.table.R | 8 ++--- .../src/R/inst/extdata/test_gatkreport.table | 20 +++++++++++++ .../src/R/inst/extdata/test_genconcord.table | 30 +++++++++++++++++++ .../gsalib/src/R/man/gsa.read.gatkreport.Rd | 4 +-- .../gsalib/src/R/man/gsa.read.gatkreportv0.Rd | 26 ++++++++++++++++ .../gsalib/src/R/man/gsa.read.gatkreportv1.Rd | 26 ++++++++++++++++ .../R/man/gsa.reshape.concordance.table.Rd | 28 ++++++++--------- public/gsalib/src/R/man/gsalib-internal.Rd | 7 +++++ .../gsalib/src/R/man/test_gatkreport.table.Rd | 13 ++++++++ .../gsalib/src/R/man/test_genconcord.table.Rd | 13 ++++++++ 10 files changed, 155 insertions(+), 20 deletions(-) create mode 100644 public/gsalib/src/R/inst/extdata/test_gatkreport.table create mode 100644 public/gsalib/src/R/inst/extdata/test_genconcord.table create mode 100644 public/gsalib/src/R/man/gsa.read.gatkreportv0.Rd create mode 100644 public/gsalib/src/R/man/gsa.read.gatkreportv1.Rd create mode 100644 public/gsalib/src/R/man/gsalib-internal.Rd create mode 100644 public/gsalib/src/R/man/test_gatkreport.table.Rd create mode 100644 public/gsalib/src/R/man/test_genconcord.table.Rd diff --git a/public/gsalib/src/R/R/gsa.reshape.concordance.table.R b/public/gsalib/src/R/R/gsa.reshape.concordance.table.R index 46c3a9e93..9b53d8714 100644 --- a/public/gsalib/src/R/R/gsa.reshape.concordance.table.R +++ b/public/gsalib/src/R/R/gsa.reshape.concordance.table.R @@ -1,9 +1,9 @@ -gsa.reshape.concordance.table <- function(data, table.name="GenotypeConcordance_Counts", sample.name="ALL") { +gsa.reshape.concordance.table <- function(report, table.name="GenotypeConcordance_Counts", sample.name="ALL") { if (!is.null(table.name)) { - data <- data[[table.name]] + data <- report[[table.name]] } - if (is.null(data)) { - return NULL + if (is.null(table.name)) { + data <- report } d <- data[data$Sample==sample.name,2:(length(data[1,])-1)] diff --git a/public/gsalib/src/R/inst/extdata/test_gatkreport.table b/public/gsalib/src/R/inst/extdata/test_gatkreport.table new file mode 100644 index 000000000..876912673 --- /dev/null +++ b/public/gsalib/src/R/inst/extdata/test_gatkreport.table @@ -0,0 +1,20 @@ +#:GATKReport.v1.0:2 +#:GATKTable:true:2:9:%.18E:%.15f:; +#:GATKTable:ErrorRatePerCycle:The error rate per sequenced position in the reads +cycle errorrate.61PA8.7 qualavg.61PA8.7 +0 7.451835696110506E-3 25.474613284804366 +1 2.362777171937477E-3 29.844949954504095 +2 9.087604507451836E-4 32.875909752547310 +3 5.452562704471102E-4 34.498999090081895 +4 9.087604507451836E-4 35.148316651501370 +5 5.452562704471102E-4 36.072234352256190 +6 5.452562704471102E-4 36.121724890829700 +7 5.452562704471102E-4 36.191048034934500 +8 5.452562704471102E-4 36.003457059679770 + +#:GATKTable:false:2:3:%s:%c:; +#:GATKTable:ExampleTable:This is an old-style table +key column +1:1000 T +1:1001 A +1:1002 C diff --git a/public/gsalib/src/R/inst/extdata/test_genconcord.table b/public/gsalib/src/R/inst/extdata/test_genconcord.table new file mode 100644 index 000000000..8748c88e2 --- /dev/null +++ b/public/gsalib/src/R/inst/extdata/test_genconcord.table @@ -0,0 +1,30 @@ +#:GATKReport.v1.1:5 +#:GATKTable:20:2:%s:%.3f:%.3f:%.3f:%.3f:%.3f:%.3f:%.3f:%.3f:%.3f:%.3f:%.3f:%.3f:%.3f:%.3f:%.3f:%.3f:%.3f:%.3f:%.3f:; +#:GATKTable:GenotypeConcordance_CompProportions:Per-sample concordance tables: proportions of genotypes called in comp +Sample NO_CALL_HOM_REF NO_CALL_HET NO_CALL_HOM_VAR HOM_REF_HOM_REF HOM_REF_HET HOM_REF_HOM_VAR HET_HOM_REF HET_HET HET_HOM_VAR HOM_VAR_HOM_REF HOM_VAR_HET HOM_VAR_HOM_VAR UNAVAILABLE_HOM_REF UNAVAILABLE_HET UNAVAILABLE_HOM_VAR MIXED_HOM_REF MIXED_HET MIXED_HOM_VAR Mismatching_Alleles +ALL 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.007 0.000 0.000 0.001 0.013 0.000 0.992 0.986 0.000 0.000 0.000 0.000 +NA12878 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.007 0.000 0.000 0.001 0.013 0.000 0.992 0.986 0.000 0.000 0.000 0.000 + +#:GATKTable:38:2:%s:%d:%d:%d:%d:%d:%d:%d:%d:%d:%d:%d:%d:%d:%d:%d:%d:%d:%d:%d:%d:%d:%d:%d:%d:%d:%d:%d:%d:%d:%d:%d:%d:%d:%d:%d:%d:%d:; +#:GATKTable:GenotypeConcordance_Counts:Per-sample concordance tables: comparison counts +Sample NO_CALL_NO_CALL NO_CALL_HOM_REF NO_CALL_HET NO_CALL_HOM_VAR NO_CALL_UNAVAILABLE NO_CALL_MIXED HOM_REF_NO_CALL HOM_REF_HOM_REF HOM_REF_HET HOM_REF_HOM_VAR HOM_REF_UNAVAILABLE HOM_REF_MIXED HET_NO_CALL HET_HOM_REF HET_HET HET_HOM_VAR HET_UNAVAILABLE HET_MIXED HOM_VAR_NO_CALL HOM_VAR_HOM_REF HOM_VAR_HET HOM_VAR_HOM_VAR HOM_VAR_UNAVAILABLE HOM_VAR_MIXED UNAVAILABLE_NO_CALL UNAVAILABLE_HOM_REF UNAVAILABLE_HET UNAVAILABLE_HOM_VAR UNAVAILABLE_UNAVAILABLE UNAVAILABLE_MIXED MIXED_NO_CALL MIXED_HOM_REF MIXED_HET MIXED_HOM_VAR MIXED_UNAVAILABLE MIXED_MIXED Mismatching_Alleles +ALL 0 0 0 0 0 0 0 0 0 0 0 0 0 0 13463 90 3901 0 0 0 2935 18144 4448 0 0 0 2053693 1326112 11290 0 0 0 0 0 0 0 16 +NA12878 0 0 0 0 0 0 0 0 0 0 0 0 0 0 13463 90 3901 0 0 0 2935 18144 4448 0 0 0 2053693 1326112 11290 0 0 0 0 0 0 0 16 + +#:GATKTable:20:2:%s:%.3f:%.3f:%.3f:%.3f:%.3f:%.3f:%.3f:%.3f:%.3f:%.3f:%.3f:%.3f:%.3f:%.3f:%.3f:%.3f:%.3f:%.3f:%.3f:; +#:GATKTable:GenotypeConcordance_EvalProportions:Per-sample concordance tables: proportions of genotypes called in eval +Sample HOM_REF_NO_CALL HOM_REF_HOM_REF HOM_REF_HET HOM_REF_HOM_VAR HOM_REF_UNAVAILABLE HOM_REF_MIXED HET_NO_CALL HET_HOM_REF HET_HET HET_HOM_VAR HET_UNAVAILABLE HET_MIXED HOM_VAR_NO_CALL HOM_VAR_HOM_REF HOM_VAR_HET HOM_VAR_HOM_VAR HOM_VAR_UNAVAILABLE HOM_VAR_MIXED Mismatching_Alleles +ALL 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.771 0.005 0.224 0.000 0.000 0.000 0.115 0.711 0.174 0.000 0.000 +NA06989 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.771 0.005 0.224 0.000 0.000 0.000 0.115 0.711 0.174 0.000 0.000 + +#:GATKTable:4:2:%s:%.3f:%.3f:%.3f:; +#:GATKTable:GenotypeConcordance_Summary:Per-sample summary statistics: NRS, NRD, and OGC +Sample Non-Reference Sensitivity Non-Reference Discrepancy Overall_Genotype_Concordance +ALL 0.010 0.087 0.913 +NA06989 0.010 0.087 0.913 + +#:GATKTable:6:1:%d:%d:%d:%d:%d:%d:; +#:GATKTable:SiteConcordance_Summary:Site-level summary statistics +ALLELES_MATCH EVAL_SUPERSET_TRUTH EVAL_SUBSET_TRUTH ALLELES_DO_NOT_MATCH EVAL_ONLY TRUTH_ONLY + 34632 0 0 16 8349 3391095 + diff --git a/public/gsalib/src/R/man/gsa.read.gatkreport.Rd b/public/gsalib/src/R/man/gsa.read.gatkreport.Rd index 28a147689..8551732c7 100644 --- a/public/gsalib/src/R/man/gsa.read.gatkreport.Rd +++ b/public/gsalib/src/R/man/gsa.read.gatkreport.Rd @@ -15,7 +15,7 @@ The path to the GATKReport file. } } \details{ -The GATKReport format replaces the multi-file output format used by many GATK tools and provides a single, consolidated file format. This format accommodates multiple tables and is still R-loadable through this function. +The GATKReport format replaces the multi-file output format used previously by many GATK tools and provides a single, consolidated file format. This format accommodates multiple tables and is still R-loadable through this function. } \value{ Returns a LIST object, where each key is the TableName and the value is the data.frame object with the contents of the table. If multiple tables with the same name exist, each one after the first will be given names of TableName.v1, TableName.v2, ..., TableName.vN. @@ -30,7 +30,7 @@ Kiran Garimella This function accepts different versions of the GATKReport format by making internal calls to gsa.read.gatkreportv0() or gsa.read.gatkreportv1() as appropriate. } \examples{ -test_file = system.file("inst", "extdata", "test_gatkreport.table", package = "gsalib"); +test_file = system.file("extdata", "test_gatkreport.table", package = "gsalib"); report = gsa.read.gatkreport(test_file); } \keyword{ manip } diff --git a/public/gsalib/src/R/man/gsa.read.gatkreportv0.Rd b/public/gsalib/src/R/man/gsa.read.gatkreportv0.Rd new file mode 100644 index 000000000..978a5afad --- /dev/null +++ b/public/gsalib/src/R/man/gsa.read.gatkreportv0.Rd @@ -0,0 +1,26 @@ +\name{gsa.read.gatkreportv0} +\alias{gsa.read.gatkreportv0} +\title{ +Function to read in an old-style GATKReport +} +\description{ +This function reads in data from a version 0.x GATKReport. It should not be called directly; instead, use gsa.read.gatkreport() +} +\usage{ +gsa.read.gatkreportv0(lines) +} +\arguments{ + \item{lines}{ +The lines read in from the input file. +} +} +\value{ +Returns a LIST object, where each key is the TableName and the value is the data.frame object with the contents of the table. If multiple tables with the same name exist, each one after the first will be given names of TableName.v1, TableName.v2, ..., TableName.vN. +} +\references{ +http://www.broadinstitute.org/gatk/guide/article?id=1244 +} +\author{ +Kiran Garimella +} +\keyword{ manip } diff --git a/public/gsalib/src/R/man/gsa.read.gatkreportv1.Rd b/public/gsalib/src/R/man/gsa.read.gatkreportv1.Rd new file mode 100644 index 000000000..b9a1add13 --- /dev/null +++ b/public/gsalib/src/R/man/gsa.read.gatkreportv1.Rd @@ -0,0 +1,26 @@ +\name{gsa.read.gatkreportv1} +\alias{gsa.read.gatkreportv1} +\title{ +Function to read in a new-style GATKReport +} +\description{ +This function reads in data from a version 1.x GATKReport. It should not be called directly; instead, use gsa.read.gatkreport() +} +\usage{ +gsa.read.gatkreportv1(lines) +} +\arguments{ + \item{lines}{ +The lines read in from the input file. +} +} +\value{ +Returns a LIST object, where each key is the TableName and the value is the data.frame object with the contents of the table. If multiple tables with the same name exist, each one after the first will be given names of TableName.v1, TableName.v2, ..., TableName.vN. +} +\references{ +http://www.broadinstitute.org/gatk/guide/article?id=1244 +} +\author{ +Kiran Garimella +} +\keyword{ manip } diff --git a/public/gsalib/src/R/man/gsa.reshape.concordance.table.Rd b/public/gsalib/src/R/man/gsa.reshape.concordance.table.Rd index f3e85047a..ba20d843f 100644 --- a/public/gsalib/src/R/man/gsa.reshape.concordance.table.Rd +++ b/public/gsalib/src/R/man/gsa.reshape.concordance.table.Rd @@ -7,17 +7,17 @@ Reshape a Concordance Table Given a GATKReport generated by GenotypeConcordance (as output by \code{gsa.read.gatkreport}), this function reshapes the concordance for a specified sample into a matrix with the EvalGenotypes in rows and the CompGenotypes in columns (see the documentation for GenotypeConcordance for the definition of Eval and Comp) } \usage{ -gsa.reshape.concordance.table(x, table="GenotypeConcordance_Counts", sample.name="ALL") +gsa.reshape.concordance.table(report, table.name="GenotypeConcordance_Counts", sample.name="ALL") } \arguments{ - \item{x}{ -A GATKReport as output by \code{gsa.read.gatkreport}. If \code{table} is \code{NULL}, \code{x} is assumed to be the vector of concordance values to reshape. + \item{report}{ +A GATKReport as output by \code{gsa.read.gatkreport}. If \code{table.name} is \code{NULL}, \code{report} is assumed to be the vector of concordance values to reshape. } - \item{table}{ -The table name in the GATKReport to reshape. Defaults to "GenotypeConcordance_Counts", but could also be one of the proportion tables ("GenotypeConcordance_EvalProportions", "GenotypeConcordance_CompProportions"). This value can also be \code{NULL}, in which case \code{x} is reshaped directly. + \item{table.name}{ +The table name in the GATKReport to reshape. Defaults to "GenotypeConcordance_Counts", but could also be one of the proportion tables ("GenotypeConcordance_EvalProportions", "GenotypeConcordance_CompProportions"). This value can also be \code{NULL}, in which case \code{report} is reshaped directly. } \item{sample.name}{ -The sample name within \code{table} to use. +The sample name within \code{table.name} to use. } } \value{ @@ -31,18 +31,18 @@ Phillip Dexheimer \code{\link{gsa.read.gatkreport}} } \examples{ -test_file = system.file("inst", "extdata", "test_gatkreport.table", package = "gsalib") +test_file = system.file("extdata", "test_genconcord.table", package = "gsalib") report = gsa.read.gatkreport(test_file) gsa.reshape.concordance.table(report) ## Output looks like: -## CompGenotypes +## CompGenotypes ##EvalGenotypes NO_CALL HOM_REF HET HOM_VAR UNAVAILABLE MIXED -## NO_CALL 0 0 0 0 0 0 -## HOM_REF 0 2 0 0 0 0 -## HET 0 3 0 0 0 0 -## HOM_VAR 0 2 0 0 0 0 -## UNAVAILABLE 0 0 0 0 0 0 -## MIXED 0 0 0 0 0 0 +## NO_CALL 0 0 0 0 0 0 +## HOM_REF 0 0 0 0 0 0 +## HET 0 0 13463 90 3901 0 +## HOM_VAR 0 0 2935 18144 4448 0 +## UNAVAILABLE 0 0 2053693 1326112 11290 0 +## MIXED 0 0 0 0 0 0 } \keyword{ manip } diff --git a/public/gsalib/src/R/man/gsalib-internal.Rd b/public/gsalib/src/R/man/gsalib-internal.Rd new file mode 100644 index 000000000..3ba87092d --- /dev/null +++ b/public/gsalib/src/R/man/gsalib-internal.Rd @@ -0,0 +1,7 @@ +\name{gsalib-internal} +\title{Internal gsalib objects} +\alias{.gsa.assignGATKTableToEnvironment} +\alias{.gsa.splitFixedWidth} +\description{Internal gsalib objects.} +\details{These are not to be called by the user.} +\keyword{internal} \ No newline at end of file diff --git a/public/gsalib/src/R/man/test_gatkreport.table.Rd b/public/gsalib/src/R/man/test_gatkreport.table.Rd new file mode 100644 index 000000000..c064da4a6 --- /dev/null +++ b/public/gsalib/src/R/man/test_gatkreport.table.Rd @@ -0,0 +1,13 @@ +\name{gatkreport_test_v1.table} +\docType{data} +\alias{gatkreport_test_v1.table} +\title{Test table for version 1.x GATKReport} +\description{ + This is a new-style GATKReport. +} +\usage{gatkreport_test_v1.table} +\format{Text document containing multiple tables} +\source{GSA test data, Broad Institute} +\references{ + http://www.broadinstitute.org/gatk/guide/article?id=1244 +} diff --git a/public/gsalib/src/R/man/test_genconcord.table.Rd b/public/gsalib/src/R/man/test_genconcord.table.Rd new file mode 100644 index 000000000..f567341c1 --- /dev/null +++ b/public/gsalib/src/R/man/test_genconcord.table.Rd @@ -0,0 +1,13 @@ +\name{genotype_concordance_test.table} +\docType{data} +\alias{genotype_concordance_test.table} +\title{Test table for Genotype Concordance Table Reshape} +\description{ + This is a GATKReport output by GenotypeConcordance. +} +\usage{genotype_concordance_test.table} +\format{Text document containing multiple tables} +\source{GSA test data, Broad Institute} +\references{ + http://www.broadinstitute.org/gatk/guide/article?id=1244 +}