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Changelog

Source: NEWS.md

iscream 1.1.8

INTERNAL

  • Remove an unused debug string for printing the locus ID from src/query_all.cpp

DOCUMENTATION

  • Use blockquote the “Getting Started” vignette to call out the note about chromosome formatting in input regions - chr1 vs 1.

iscream 1.1.7

BUG FIXES

  • Fix htslib_version() to return the version as a string instead of simply printing it to allow programmatic checks for libdeflate presence.

  • iscream now informs users whether they have libdeflate-enabled htslib on package load.

iscream 1.1.6

BUG FIXES

  • Fix a check for missing input files by correcting checking the filepath vector length

INTERNAL

  • Use inherits(x, "data.frame") instead of "data.frame" %in% class(x)"

iscream 1.1.5

BREAKING CHANGES to summarize_regions() and summarize_meth_regions():

  • The summary output now has position as chromosome, start, and end columns instead of just a feature column with the position string. This allows direct conversion to GRanges objects without having to use rownames. It is still possible to use chromosome names as the input query regions (“chr1”), the start and end in those cases will be NA.

  • The feature column is now populated only if the input regions are named, if a vector, or the feature_col argument is set to a column for data.frame/GRanges inputs.

  • The count column from summarize_meth_regions() is now named count instead of cpg_count.

  • These functions now return a data.table instead of a data.frame to allow for faster in-place modifications and consistency with tabix() output. Use data.table::setDF() to convert to a data.frame in-place.

BUG FIXES

  • Rownames are no longer set for the summarize_regions() or summarize_meth_regions() output using the input region strings as these were repeating and not unique. It was only possible because they were set from the C++ scope instead of R.

ENHANCEMENTS

  • summarize_regions() and summarize_meth_regions() now support the following new functions, inspired by bedtools map:

    • Population standard deviation (pstddev)
    • First element (first)
    • Last element (last)
    • Mode (mode)
    • Anti-mode (antimode)
    • Absolute min (absmin)
    • Absolute max (absmax)
    • Count of unique values (count_distinct)

  • get_granges_string() can now extract names from its mcols using a feature_col argument as in get_df_string() - names were previously pulled only from names(). This means GRanges inputs to summarize_regions() can have the feature_col in its mcols rather than just as its names.

DOCUMENTATION

  • Update Zenodo URLs in vignettes to the updated record: https://zenodo.org/records/18089082. The genes.bed file used in vignette("performance") now contains the gene names that the vignette references.

INTERNAL

  • Refactored summarize_regions to collect similar validation and regions parsing functions

  • tabix() writes the input regions of interest to disk only once instead of doing it for every file

iscream 1.1.4

BUG FIX

  • Reduced the minimum R version from 4.5 to 4.4

iscream 1.1.3

DOCUMENTATION

  • Document how to make use of strand information with tabix()
  • Improve wording of tabix()‘s’ aligner and col.names documentation

iscream 1.1.2

  • Fix typo in error message from thread count checks

iscream 1.1.1

BUG FIXES

  • Fix configure to correctly check htslib version when rhtslib is not used and not issue spurious warnings

iscream 1.0.0

  • First Bioconductor release

iscream 0.99.9

DOCUMENTATION

  • Vignettes suppress long startup messages

  • Updated run-times and plots in tabix vs Rsamtools vignette

iscream 0.99.8

BUG FIXES

  • For tabix(), converting GRanges inputs of width 1 now returns them as chr:start-start instead of chr:start which was invalid for the htslib API and caused a block of records to be returned instead of just the locus.

iscream 0.99.7

BREAKING CHANGES

  • Functions that return GenomicRanges or SummarizedExperiment will fail if those packages are not loaded so that users don’t receive objects they can’t interact with

DOCUMENTATION

  • bsseq creation now runs for the make_mat_bsseq example

iscream 0.99.6

BREAKING CHANGES

  • make_bsseq_mat changed to make_mat_bsseq for consistency with other matrix creating functions

BUG FIXES

  • Fixed MacOS and clang issues (version checking, using the correct linkage tools) in configuration script

  • Explicitly coerce path to string for bedfile prefix extraction in Cpp_summarize_regions

ENHANCEMENTS

  • Added windows as supported platform but without multithreading support

  • pbapply progress bar added to tabix() functions

INTERNAL

  • Explicitly return result from tabix.single helper function.

  • Removed unused C++ variables

  • file.path used instead of pasting paths

DOCUMENTATION

  • bsseq added to Suggests to run in examples and vignettes

  • Changed all \dontrun to \donttest

  • All vignettes set to BiocStyle

  • BiocFileCache now used for all vignette file downloads

  • Reading the genes file in the “performance” vignette fixed to read only three columns

  • Added more information on bitpacking limits for make_mat_bsseq

  • Allowed creation of BSseq objects in data structures vignette

  • Package description updated to add information about methylation support

  • Replaced all references to CpG with more general methylation

  • Added CpH as supported in documentation

iscream 0.99.5

INTERNAL

  • tabix executable-dependent tests are skipped if tabix is not installed

iscream 0.99.4

  • tabix executable added to SystemRequirements

iscream 0.99.1

  • Updated LICENSE files for R CMD check

iscream 0.99.0

  • Pre-release for manuscript and Bioconductor review