1. gmapR
  2. inst
  3. unitTests
  4. test_BamTallyParam.R
Browse code

support new version of bam_tally

Michael Lawrence authored on 12/06/2019 22:48:54
Showing 1 changed files
inst/unitTests/test_BamTallyParam.R
History View file @ c3db7e3
... ... 
@@ -8,9 +8,9 @@ test_BamTallyParam <- function() {
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                minimum_mapq = 0L,
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                concordant_only = FALSE, unique_only = FALSE,
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                primary_only = FALSE, ignore_duplicates = FALSE,
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-               min_depth = 0L, variant_strand = 0L,
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+               min_depth = 0L, variant_strand = 0L, variant_pct = 0,
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                ignore_query_Ns = FALSE,
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-               indels = FALSE, include_soft_clips = 0L,
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+               indels = FALSE, min_softclip = 0L, max_softclip = 0L,
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                xs = FALSE, read_pos = FALSE, min_base_quality = 0L,
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                noncovered = FALSE, nm = FALSE)
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   which <- TP53Which()
Browse code

general cleanup and fixes, doc updates

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/gmapR@111183 bc3139a8-67e5-0310-9ffc-ced21a209358

Michael Lawrence authored on 03/12/2015 21:11:09
Showing 1 changed files
inst/unitTests/test_BamTallyParam.R
History View file @ f053c5f
... ... 
@@ -10,7 +10,9 @@ test_BamTallyParam <- function() {
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                primary_only = FALSE, ignore_duplicates = FALSE,
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                min_depth = 0L, variant_strand = 0L,
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                ignore_query_Ns = FALSE,
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-               indels = FALSE, include_soft_clips = 0L)
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+               indels = FALSE, include_soft_clips = 0L,
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+               xs = FALSE, read_pos = FALSE, min_base_quality = 0L,
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+               noncovered = FALSE, nm = FALSE)
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   which <- TP53Which()
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   wicked.which <- renameSeqlevels(which, c(TP53 = "chr1"))
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Browse code

add codon tally support. No vbump yet

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/gmapR@93316 bc3139a8-67e5-0310-9ffc-ced21a209358

Gabriel Becker authored on 11/08/2014 23:42:48
Showing 1 changed files
inst/unitTests/test_BamTallyParam.R
History View file @ c78be69
... ... 
@@ -10,8 +10,7 @@ test_BamTallyParam <- function() {
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                primary_only = FALSE, ignore_duplicates = FALSE,
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                min_depth = 0L, variant_strand = 0L,
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                ignore_query_Ns = FALSE,
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-               indels = FALSE, include_soft_clips = 0L,
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-               count_xs = FALSE, noncovered = FALSE)
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+               indels = FALSE, include_soft_clips = 0L)
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   which <- TP53Which()
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   wicked.which <- renameSeqlevels(which, c(TP53 = "chr1"))
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Browse code

fix BamTallyParam test

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/gmapR@90425 bc3139a8-67e5-0310-9ffc-ced21a209358

Michael Lawrence authored on 16/05/2014 21:33:54
Showing 1 changed files
inst/unitTests/test_BamTallyParam.R
History View file @ d96aab2
... ... 
@@ -10,7 +10,8 @@ test_BamTallyParam <- function() {
10 10 
                primary_only = FALSE, ignore_duplicates = FALSE,
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                min_depth = 0L, variant_strand = 0L,
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                ignore_query_Ns = FALSE,
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-               indels = FALSE, include_soft_clips = 0L)
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+               indels = FALSE, include_soft_clips = 0L,
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+               count_xs = FALSE, noncovered = FALSE)
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   which <- TP53Which()
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   wicked.which <- renameSeqlevels(which, c(TP53 = "chr1"))
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Browse code

fix unit test for addition of remove_soft_clips

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/gmapR@88622 bc3139a8-67e5-0310-9ffc-ced21a209358

Michael Lawrence authored on 08/04/2014 22:43:12
Showing 1 changed files
inst/unitTests/test_BamTallyParam.R
History View file @ d3ef88e
... ... 
@@ -10,7 +10,7 @@ test_BamTallyParam <- function() {
10 10 
                primary_only = FALSE, ignore_duplicates = FALSE,
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                min_depth = 0L, variant_strand = 0L,
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                ignore_query_Ns = FALSE,
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-               indels = FALSE)
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+               indels = FALSE, include_soft_clips = 0L)
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   which <- TP53Which()
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   wicked.which <- renameSeqlevels(which, c(TP53 = "chr1"))
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Browse code

updates to tests

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/gmapR@79522 bc3139a8-67e5-0310-9ffc-ced21a209358

Michael Lawrence authored on 17/08/2013 01:41:06
Showing 1 changed files
inst/unitTests/test_BamTallyParam.R
History View file @ 99c8aa8
... ... 
@@ -3,7 +3,8 @@ test_BamTallyParam <- function() {
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   on.exit(options(warn = 0))
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   genome <- TP53Genome()
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   genome.name <- genome(genome)
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-  param <- new("BamTallyParam", genome = genome, which = RangesList(),
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+  param <- new("BamTallyParam", genome = genome,
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+               which = gmapR:::normArgWhich(GRanges(), genome),
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                minimum_mapq = 0L,
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                concordant_only = FALSE, unique_only = FALSE,
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                primary_only = FALSE, ignore_duplicates = FALSE,
Browse code

add some unit tests for BamTallyParam

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/gmapR@78420 bc3139a8-67e5-0310-9ffc-ced21a209358

Michael Lawrence authored on 14/07/2013 00:31:18
Showing 1 changed files
inst/unitTests/test_BamTallyParam.R
History View file @ 23e2256
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new file mode 100644
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@@ -0,0 +1,31 @@
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+test_BamTallyParam <- function() {
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+  options(warn = 2)
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+  on.exit(options(warn = 0))
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+  genome <- TP53Genome()
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+  genome.name <- genome(genome)
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+  param <- new("BamTallyParam", genome = genome, which = RangesList(),
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+               minimum_mapq = 0L,
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+               concordant_only = FALSE, unique_only = FALSE,
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+               primary_only = FALSE, ignore_duplicates = FALSE,
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+               min_depth = 0L, variant_strand = 0L,
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+               ignore_query_Ns = FALSE,
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+               indels = FALSE)
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+  which <- TP53Which()
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+  wicked.which <- renameSeqlevels(which, c(TP53 = "chr1"))
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+
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+  checkException(BamTallyParam(), silent = TRUE)
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+  checkException(BamTallyParam(5), silent = TRUE)
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+
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+  checkIdentical(BamTallyParam(genome.name), param)
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+  checkException(BamTallyParam(genome, IRanges(1, 10)), silent = TRUE)
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+  checkException(BamTallyParam(genome, wicked.which), silent = TRUE)
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+  param@which <- gmapR:::normArgWhich(which, genome)
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+  checkIdentical(BamTallyParam(genome, which), param)
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+  checkException(BamTallyParam(genome, concordant_only = NA), silent = TRUE)
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+  checkException(BamTallyParam(genome, unique_only = rep(FALSE, 2)),
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+                 silent = TRUE)
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+  checkException(BamTallyParam(genome, min_depth = -1), silent = TRUE)
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+  checkException(BamTallyParam(genome, variant_strand = 5), silent = TRUE)
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+  param@variant_strand <- 2L
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+  checkIdentical(BamTallyParam(genome, which, variant_strand = 2), param)
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+}