Updated method functions for plotting SBS96, SBS192, DBS78 and ID counts catalog; the counts shown on the plot are sum of absolute value of each peak.
Updated internal function ConvertCatalogToSigProfilerFormat to support
conversion from ICAMS SBS192 and SBS1536 catalog to SigPro format.
Updated exported function ReadCatalog to support reading in SBS1536 catalog
in SigPro format.
catalog.row.order$ID166 and catalog.row.headers$ID166
for genic-intergenic indel catalog (ID166).Added new exported function IsICAMSCatalog to check whether an R object
contains one of the ICAMS catalog classes.
Added new internal function SelectVariantsByChromName.
Added new argument chr.names.to.process to exported functions
VCFsToCatalogs, ReadAndSplitVCFs, SplitListOfVCFs, VCFsToCatalogsAndPlotToPdf and
VCFsToZipFile that allow users to only select and process variants from
specified chromosome names.
Added a section Subscripting catalogs in ICAMS package documentation.
Nongenic region to Intergenic region.Added new data catalog.row.order$ID166 and catalog.row.headers$ID166
for genic-intergenic indel catalog.
Added functionality for ReadCatalog to read in genic-intergenic indel
catalog (ID166).
Added functionality for WriteCatalog to write genic-intergenic indel
catalog (ID166) to CSV file.
Added cbind and [ method for ID166Catalog.
Added functionality for PlotCatalog and PlotCatalogToPdf to plot
genic-intergenic indel catalog (ID166).
Updated function PlotCatalog to change options("digits") temporarily to
prevent weird y axis labels.
Updated function AnnotateSBSVCF not to call CheckSeqContextInVCF as this
check will done later at function CreateOneColSBSMatrix.
Updated exported functions' examples not to use deprecated functions.
Updated internal function StandardChromNameNew to also discard variants
whose chromosome names contain "fix" or "alt".
Updated internal function ReadVCF not to calculate VAF for multiple
alternative variants in freebayes VCF to avoid warning messages.
Updated code in exported function GetFreebayesVAF to improve time
performance dramatically (about 5 times faster) by using regular expressions for
pattern matching and retrieving.
Updated documentation of argument max.vaf.diff in various functions
informing users that they can specify a negative value (e.g. -1) to suppress
merging adjacent SBSs to DBS.
Added a new dependency package fuzzyjoin.
Added new internal function DefaultFilterStatus to automatically infer
filter.status according to variant.caller.
Fixed a bug in internal function AddTranscript caused by data.table::foverlaps
producing memory errors when the input VCF has many variants (e.g. >70000 lines).
Used fuzzyjoin::genome_left_join instead.
Fixed a bug in internal function MakeDataFrameFromVCF when renaming column
#CHROM to CHROM.
Fixed a bug in internal function CheckAndRemoveDiscardedVariants to remove
variants with ambiguous REF bases (not A, C, G, T).
Fixed a bug in exported function TransformCatalog when user specifies
ref.genome as a character string. No longer raise an error when user did not
install the BSgenome package.
InferRefGenomeName to infer reference genome
name from a character string.IsRefGenomeInstalled to check whether the
BSgenome package is installed. If not, the returned catalog will have
NULL ref.genome attribute.Fixed a bug in internal function AddTranscript when setting the data table
new names.
Updated two internal functions GeneratePCAWGAliquotID and
GeneratePCAWGAliquotID2.
Corrected error in the original Excel file showing PCAWG7 indel classification. Updated the links in documentation pointing to the correct Excel file. Added a new column showing the ICAMS ID catalog row name.
Set a minimum value of 21 for seq.context.width in function AnnotateIDVCF to facilitate
extended sequence context analysis.
Added examples to two new exported functions SymmetricalContextsFor1BPIndel
and GeneratePlotPFMmatrix.
Added new exported function HaplotypePlot.
Added two new internal functions RenameColumnsWithNameStart and
RenameColumnsWithNameEnd to check whether there are column names start and
end in the original VCF. This is to avoid breaking the code in function
AddTranscript.
Added two new dependency packages lifecycle and rlang.
Soft deprecated several exported functions
MutectVCFFilesToCatalog, StrelkaIDVCFFilesToCatalog, StrelkaSBSVCFFilesToCatalogMutectVCFFilesToCatalogAndPlotToPdf, StrelkaIDVCFFilesToCatalogAndPlotToPdf, StrelkaSBSVCFFilesToCatalogAndPlotToPdfMutectVCFFilesToZipFile, StrelkaIDVCFFilesToZipFile, StrelkaSBSVCFFilesToZipFileReadAndSplitMutectVCFs, ReadAndSplitStrelkaSBSVCFs, ReadStrelkaIDVCFsFixed a bug in internal function ReadVCF when the VCF does not have column FILTER.
Updated documentation for ID that refers to small insertions and deletions.
Updated documentation for ICAMS.R that is no longer referring to some deprecated functions.
Added internal function GenerateVCFsFromIndelSimpleFiles to generate reconstructed VCFs from
indel simple files.
Updated internal function ReadVCF to check whether VCF has column FILTER. If VCF
does not have FILTER column, raise a warning and all variants will be retained.
Exported two functions ReadVCFs and SplitListOfVCFs and added examples.
Updated code in function ReadVCF for filtering out variants that do not have the value of filter.status to avoid segfaults error.
PASS to argument filter.status in several exported and internal functions.Fixed a bug in internal function CheckAndNormalizeTranCatArgs for
transforming catalog. If the target.abundance can be inferred and is different
from a supplied non-NULL value of target.abundance, no longer raise an
error. Use the supplied non-NULL value of target.abundance instead.
Updated internal function ReadBedRanges to only keep entries that are from
chromosomes 1-22 and X and Y.
SimpleReadVCF; some code simplification.always.merge.SBS to several functions.Added new internal function RetrieveNonEmptySamples to retrieve non empty samples from a catalog.
Added new internal function ConvertCatalogToSigProfilerFormat to convert ICAMS SBS96, DBS78 and ID catalog to SigProfiler format.
Updated function StandardChromName and StandardChromNameNew to remove variants
whose chromosome names contain "JH".
Updated functions VCFsToCatalogsAndPlotToPdf and VCFsToZipFile to only plot samples
that have mutations for a specific mutation class.
Enabled argument tumor.col.name and tumor.col.names in various functions to also take
in numbers as column indices.
Updated internal function MakeDataFrameFromVCF to use argument file instead of name.of.VCF to report error when the input file is not a VCF file.
Updated internal data catalog.row.headers.sp$ID83 and ICAMS.to.SigPro.ID.
MakeSBS96CatalogFromSigPro and
MakeDBS78CatalogFromSigPro for missing argument drop = FALSE when reordering
a one-column catalog.expect_equal for comparing numerical valuesTransformCatalog in case R was configured and built in a way that did not support long double.Updated documentation of ReadCatalog and ReadCatalogInternal as there are no ID96 catalogs in COSMIC v3.2.
Changed the URL of COSMIC mutational signatures page to the redirected URL.
Updated some tests for TransformCatalog in case R was configured and built in a way that did not support long double.
Added the argument strict back to ReadCatalog for backward compatibility;
strict is now ignored and deprecated.
Robustified function StandardChromNameNew to select the column which
contains chromosome names by name instead of column index.
Fixed a bug in function CheckSeqContextInVCF.
Fixed a bug in function PlotCatalog.SBS96Catalog when plotting the X axis
after setting par(tck) = 0.
Changed PlotCatalog to round the mutation counts for each main type for
SBS96, SBS192, DBS78 and ID counts catalog in case the input is reconstructed
counts catalog.
Updated function AdjustNumberOfCores not to throw a message on MS Windows machine.
Added an additional argument ylabels to PlotCatalog and PlotCatalogToPdf.
When ylabels = FALSE, don't plot the y axis labels. Implemented for SBS96Catalog, DBS78Catalog, IndelCatalog.
Enabled argument grid, uppder, xlabels in PlotCatalog and PlotCatalogToPdf
for DBS78Catalog, IndelCatalog.
ReadCatalog to import files with:
ReadCatalog function, e.g.
ReadCatalog.SBS96Catalog. Now they are in
data-raw/obsolete-files/ReadCatalogMethods.R.ConvCatalogToICAMS to convert SigProfiler/COSMIC-formatted
catalog files into ICAMS catalog objects. Now these functions are in
data-raw/obsolete-files/ConvCatalogToICAMS.R, and their functionalities are
integrated into ReadCatalog.ReadCatalog to remove rows which have NA in the data table read in. Otherwise
the number of rows will not be accurate to infer the correct catalog type.InferClassOfCatalogForRead to data-raw/obsolete-files/InferClassOfCatalogForRead.R.CreateOneColDBSMatrix when returning 1-column
DBS144 matrix with all values being 0 and the correct row labels.Added an additional argument tmpdir in function AddRunInformation.
Updated function CheckAndRemoveDiscardedVariants and MakeDataFrameFromVCF to check
for variants that have same REF and ALT.
Create new temp directory when generating zip archive from VCFs to avoid zipping unnecessary files in the output.
Fixed a bug in function AddRunInformation for allowing ref.genome to be a
Bioconductor package.
Fixed bugs in function CreateOneColSBSMatrix, CreateOneColDBSMatrix and
CreateOneColIDMatrix when the variants in the input vcfs should all be
discarded.
Updated function CheckAndFixChrNames to give a warning instead of an error
when "23" and "X" or "24" and "Y" appear on the chromosome names on the VCF at
the same time. CheckAndFixChrNames will change "23" to "X" or "24" to "Y"
internally for downstream processing.
Changed some code in function AddTranscript, CreateOneColSBSMatrix,
CreateOneColDBSMatrix to use functions from package dplyr instead of
data.table due to segfault error.
RemoveRowsWithDuplicatedCHROMAndPOSNew to remove variants
that have same CHROM, POS, REF.files in function VCFsToZipFile.Fixed a bug in ReadAndSplitVCFs for merging adjacent SBSs into DBS when variant.caller is mutect.
Fixed a bug inCheckAndRemoveDiscardedVariants for removing wrong DBS variants.
CheckAndRemoveDiscardedVariants to remove wrong DBS variants that have same base in the same position in REF and ALT (e.g. TA > TT or GT > CT).name.of.VCF in function MakeDataFrameFromVCF
for better error reporting.Updated function MakeDataFrameFromVCF for better error reporting when reading
in files that are actually not VCFs.
Updated function ReadVCFs to automatically change the number of cores to 1 on
Windows instead of throwing an error.
CheckAndFixChrNames for returning the correct number of chromosome names.stop.on.error and code tryCatch in function
VCFsToCatalogs for better tracing if the function stops on error.Added argument stop.on.error to VCFsToCatalogs; if false, return
list with single element named error.
Added new internal function CheckAndFixChrNamesForTransRanges. The
chromosome names in exported data TranscriptRanges don't have "chr". ICAMS now
will check for the chromosome names format in input vcf and update the
trans.ranges chromosome names in function AddTranscript if needed.
Added new argument name.of.VCF in function AnnotateSBSVCF and
AnnotateDBSVCF for better error reporting.
Changed return from ReadCatalog to include possible
attribute "error" and allow for not calling stop() on
error.
For a stranded catalog, as.catalog and ReadCatalog will silently convert
region = "genome" to "transcript".
Updated function AddTranscript to check whether the format of VCF chromosome
names is consistent with that in trans.ranges used.
Removed documentation warnings related to \link{BSgenome...}
Some file reorganization.
CreateOneColSBSMatrix for showing message that SBS variant
whose reference base in ref.genome does not match the reference base in the VCF
file.Enabled functions PlotCatalog and PlotCatalogToPdf to plot a numeric
matrix, numeric data.frame, or a vector denoting the mutation counts.
Added new internal function AdjustNumberOfCores to change the number of cores
automatically to 1 if the operating system is Windows.
Added test processing VCF with unknown variant caller.
Added new internal function SplitSBSVCF, SplitOneVCF, SplitListOfVCFs and VCFsToZipFileXtra, WriteSBS96CatalogAsTsv,
ReadSBS96CatalogFromTsv, GetConsensusVAF.
Added new exported function ReadAndSplitVCFs, VCFsToCatalogs, VCFsToCatalogsAndPlotToPdf and VCFsToZipFile.
Added new argument filter.status and get.vaf.function in functions ReadVCF,
ReadVCFs, ReadAndSplitVCFs, VCFsToCatalogs, VCFsToCatalogsAndPlotToPdf
and VCFsToZipFile.
Added a new internal data catalog.row.headers.SBS.96.v1.
Added new argument max.vaf.diff in internal functions SplitOneVCF, SplitListOfVCFs and exported functions ReadAndSplitVCFs, VCFsToCatalogs,
VCFsToCatalogsAndPlotToPdf and VCFsToZipFile.
Added new dependency package parallel.
Added new dependency package R.utils for data.table::fread to read gz and bz2 files directly.
Added new argument num.of.cores in internal functions ReadVCFs, SplitListOfVCFs and exported functions ReadAndSplitVCFs, VCFsToCatalogsAndPlotToPdf, VCFsToCatalogs, VCFsToZipFile, VCFsToIDCatalogs, VCFsToSBSCatalogs, VCFsToDBSCatalogs.
Added new argument ... in internal functions ReadVCF, ReadVCFs and exported functions ReadAndSplitVCFs, VCFsToCatalogsAndPlotToPdf, VCFsToCatalogs, VCFsToZipFile.
Added new argument mc.cores in internal functions GetConsensusVAF.
MakeDataFrameFromVCF to use data.table::fread instead of
read.csv.MakeDataFrameFromVCF when reading in VCF from URL.Updated function CreateOneColSBSMatrix to throw a message instead of an error when there are SBS variant whose reference base in ref.genome does not match the reference base in the VCF file.
Updated function MakeVCFDBSdf to inherit column information from original SBS VCF.
Changed the words in legend for DBS144 plot from "Transcribed", "Untranscribed" to "Transcribed strand" and "Untranscribed strand".
Updated the documentation for exported data all.abundance.
Updated function ReadCatalog.COMPOSITECatalog not to convert "::" to ".." in the column names.
Updated various functions in ICAMS to generate catalogs with zero mutation counts from empty vcfs.
Added a section "ID classification" in the documentation for exported data catalog.row.order.
New argument suppress.discarded.variants.warnings in exported
function AnnotateIDVCF with default value TRUE.
Added another paper information in AddRunInformation. "Characterization of
colibactin-associated mutational signature in an Asian oral squamous cell
carcinoma and in other mucosal tumor types", Genome Research 2020
https://doi.org/10.1101/gr.255620.119.
Changed the format of DOIs in DESCRIPTION according to CRAN policy.
Changed back the return value of ReadStrelkaIDVCFs, ReadStrelkaSBSVCFs,
ReadMutectVCFs to a list of data frames with no variants discarded.
Combined all the discarded variants from ReadAndSplitMutectVCFs and
ReadAndSplitStrelkaSBSVCFs under one element discarded.variants in the
return value. An extra column discarded.reason were added to show the details.
Updated internal functions ReadVCF and ReadVCFs not to remove any discarded
variants.
No more removal of "chr" in the CHROM column when reading in VCFs.
CheckAndReturnSBSMatrix, CheckAndReturnDBSMatrix,
CreateOneColSBSMatrix,CreateOneColDBSMatrix, VCFsToSBSCatalogs,
VCFsToDBSCatalogs.CalculateExpressionLevel for the edge case.CreateOneColIDMatrix when the ID.class contains non canonical
representation of the ID mutation type.The return value of exported function ReadStrelkaIDVCFs now sometimes
contains a new element, discarded.variants. This appears when there are
variants that were discarded immediately after reading in the VCFs. At present
these are variants that have duplicated chromosome/positions and variants that
have illegal chromosome names. This means that the user must check the return to
see if discarded.variants is present and remove it before passing the return
to a function that expects a list of VCFs. Code in ICAMS that takes lists of
VCFs already checks for this element and removes it if present.
Added argument return.annotated.vcfs to exported function
VCFsToIDCatalogs. The default value for the argument is FALSE
to be consistent with other functions.
Argument return.annotated.vcfs in functions
VCFsToSBSCatalogs,VCFsToDBSCatalogs, VCFsToIDCatalogs,
MutectVCFFilesToCatalog, MutectVCFFilesToCatalogAndPlotToPdf,
MutectVCFFilesToZipFile, StrelkaSBSVCFFilesToCatalog,
StrelkaSBSVCFFilesToCatalogAndPlotToPdf, StrelkaSBSVCFFilesToZipFile,
StrelkaIDVCFFilesToCatalog, StrelkaIDVCFFilesToCatalogAndPlotToPdf and
StrelkaIDVCFFilesToZipFile.
Argument suppress.discarded.variants.warnings in functions
ReadAndSplitMutectVCFs, ReadAndSplitStrelkaSBSVCFs,
VCFsToSBSCatalogs,VCFsToDBSCatalogs, VCFsToIDCatalogs,
MutectVCFFilesToCatalog, MutectVCFFilesToCatalogAndPlotToPdf,
MutectVCFFilesToZipFile, StrelkaSBSVCFFilesToCatalog,
StrelkaSBSVCFFilesToCatalogAndPlotToPdf, StrelkaSBSVCFFilesToZipFile,
StrelkaIDVCFFilesToCatalog, StrelkaIDVCFFilesToCatalogAndPlotToPdf and
StrelkaIDVCFFilesToZipFile.
Added documentation to exported functions ReadAndSplitStrelkaSBSVCFs,
StrelkaSBSVCFFilesToCatalog, StrelkaSBSVCFFilesToCatalogAndPlotToPdf
and StrelkaSBSVCFFilesToZipFile.
Added information on the "ID classification" in documentation
of functions generating ID catalogs, FindDelMH and FindMaxRepeatDel.
Minor changes to documentation of functions PlotCatalog, PlotCatalogToPdf,
StrelkaSBSVCFFilesToZipFile, StrelkaIDVCFFilesToZipFile and
MutectVCFFilesToZipFile.
Updated documentation for the return value of functions
StrelkaIDVCFFilesToCatalog, StrelkaIDVCFFilesToCatalogAndPlotToPdf,
StrelkaIDVCFFilesToZipFile and VCFsToIDCatalogs to make it clearer to the user.
Added new exported data of catalog row order for SBS96, SBS1536 and DBS78
in SigProfiler format to catalog.row.order.sp.
New internal function ConvertICAMSCatalogToSigProSBS96, ReadVCF, ReadVCFs.
New exported function GetFreebayesVAF for calculating variant allele
frequencies from Freebayes VCF.
New test data for Strelka mixed VCF.
Added time zone information to file "run-information.txt" when calling
functions MutectVCFFilesToZipFile, StrelkaSBSVCFFilesToZipFile and
StrelkaIDVCFFilesToZipFile.
Enabled "counts" -> "counts.signature" catalog transformation when the source catalog has NULL abundance.
Added legend for SBS192 plot and changed the legend text for SBS12 plot.
Added a second element plot.object to the return list from function
PlotCatalog for catalog types "SBS192Catalog", "DBS78Catalog", "DBS144Catalog"
and "IndelCatalog". The second element is a numeric vector giving the
coordinates of the bar midpoints, useful for adding to the graph.
Made the returns from PlotCatalog and PlotCatalogToPdf invisible.
Improved time performance of GetMutectVAF, CanonicalizeDBS, CanonicalizeQUAD.
if statements in GetCustomKmerCounts、 GetStrandedKmerCounts and
GetGenomeKmerCounts.
CreateOneColIDMatrix when there is NA ID category.
GetMutectVAF to check if the VCF is indeed a Mutect VCF.
CreateOneColDBSMatrix when the VCF does not have any variant in the
transcribed region.
CalculatePValues when there is only a single expression value.
Created an internal function MakeDataFrameFromVCF to read in data lines of a VCF.
New argument name.of.VCF in internal function CheckAndFixChrNames to make
the error message more informative.
New argument name.of.VCF in exported
function AnnotateIDVCF to make the error message more informative.
ReadStrelkaIDVCF to make the error message more informative.AnnotateIDVCF to a list. The first element annotated.vcf contains the annotated VCF. If there are rows that are discarded, the function will generate a warning and
a second element discarded.variants will be included in the returned list.flag.mismatches deprecated in exported function AnnotateIDVCF. If there are mismatches to references, the
function will automatically discard these rows. User can refer to the
element discarded.variants in the return value for the discarded variants.SplitStrelkaSBSVCF when there are no non.SBS mutations in the input.MakeDataFrameFromMutectVCF when a Mutect VCF has no meta-information lines.CreateOneColSBSMatrix when an annotated SBS VCF has variants on transcribed regions that all fall on transcripts on both strand.CreateOneColDBSMatrix when an annotated DBS VCF has variants on transcribed regions that all fall on transcripts on both strand.ReadAndSplitStrelkaSBSVCFs.MutectVCFFilesToZipFile, StrelkaSBSVCFFilesToZipFile and
StrelkaIDVCFFilesToZipFile.trans.ranges
to make it optional.name.of.VCF in internal functions
ReadStrelkaSBSVCF, ReadStrelkaIDVCF and exported function GetStrelkaVAF.flag.mismatches in functions VCFsToIDCatalogs,
MutectVCFFilesToCatalog, MutectVCFFilesToCatalogAndPlotToPdf,
MutectVCFFilesToZipFile, StrelkaIDVCFFilesToCatalog,
StrelkaIDVCFFilesToCatalogAndPlotToPdf and StrelkaIDVCFFilesToZipFile.GetStrelkaVAF andGetMutectVAF to a data frame which contains the VAF and read depth information.PlotCatalogToPdf a
list. The first element is a logical value indicating whether the plot is
successful. The second element is a list containing the strand bias statistics
(only for SBS192Catalog with "counts" catalog.type
and non-NULL abundance and argument plot.SBS12 = TRUE).PlotCatalog and PlotCatalogToPdf:
For class SBS96Catalog:
(New) Allow setting ylim and cex.
(New) For PlotCatalog (not PlotCatalogToPdf), allow plotting of a 96 x 2 catalog,
in which case behavior is a stacked bar chart.
(New) Plot x axis tick marks if xlabels is not TRUE; set par(tck = 0) to suppress.
For class IndelCatalog:
(New) Allow setting ylim.GetCustomKmerCounts.PlotTransBiasGeneExpToPdf so that ymax on the plot will be changed
based on plot.type.flat.abundance from "numeric" to
"integer".TransformCatalog; see documentation
for rationale.TransformCatalog and updated its documentation
for parameter target.abundance.CheckAndFixChrNames and updated the automated tests.TransformCatalog.GetMutectVAF and updated the warning
message to make it more informative.cbind
to check the attributes of the incoming catalogs and assign attributes accordingly.TransformCatalog to check the attributes of the catalog to be
transformed in the first place.AnnotateSBSVCF, AnnotateDBSVCF and
AnnotateIDVCF.PlotTransBiasGeneExp and PlotTransBiasGeneExpToPdf.names.of.VCFs in functions
ReadAndSplitMutectVCFs, ReadAndSplitStrelkaSBSVCFs, ReadStrelkaIDVCFs,
MutectVCFFilesToCatalog, MutectVCFFilesToCatalogAndPlotToPdf,
StrelkaIDVCFFilesToCatalog, StrelkaIDVCFFilesToCatalogAndPlotToPdf,
StrelkaSBSVCFFilesToCatalog and StrelkaSBSVCFFilesToCatalogAndPlotToPdf
for users to specify the names of samples in the VCF files.as.catalog.gene.expression.data.HepG2 and
gene.expression.data.MCF10A.tumor.col.names in functions
ReadAndSplitMutectVCFs, MutectVCFFilesToCatalog and
MutectVCFFilesToCatalogAndPlotToPdf to specify the column of the VCF
that contains sequencing statistics such as sequencing depth; this column
is often called "unknown" in Mutect.MutectVCFFilesToCatalog,
MutectVCFFilesToCatalogAndPlotToPdf, StrelkaSBSVCFFilesToCatalog,
StrelkaSBSVCFFilesToCatalogAndPlotToPdf, VCFsToSBSCatalogs,
VCFsToDBSCatalogs, ReadCatalog informing the user how to change
attributes of the generated catalog.VCFsToIDCatalogs, StrelkaIDVCFFilesToCatalog
and StrelkaIDVCFFilesToCatalogAndPlotToPdf a list; 1st element is the
spectrum catalog (previously the only return); 2nd element is a list of
VCFs with additional annotations.PlotCatalog a list. The first element is
a logical value indicating whether the plot is successful. The second element
is a numeric vector giving the coordinates of all the bar midpoints drawn,
useful for adding to the graph (only implemented for SBS96Catalog).output.file argument in
MutectVCFFilesToCatalogAndPlotToPdf, StrelkaSBSVCFFilesToCatalogAndPlotToPdf,
and StrelkaIDVCFFilesToCatalogAndPlotToPdf
so that an indicator of the catalog type plus ".pdf" is simply
appended to the base output.file name. Also made this argument
optional with sensible default behavior.trans.ranges.GRCh37, trans.ranges.GRCh38 and trans.ranges.GRCm38.FindDelMH, cryptic repeats (i.e. un-normalized deletions in a repeat
such as GAGG deleted from CCCAGGGAGGGTCCC, which should be normalized
to a deletion of AGGG) are now ignored with a warning rather than
causing a stop.FindDelMH, which previously did not flag the
cryptic repeat in what is now the second example in the function documentation.as.catalog supports creation of the catalog from a vector (interpreted
as a 1-column matrix) and optionally infers the class from the
number of rows in the input.