Changes in version 1.3.13 (2018-10-22):

    o   fixed bug in `create_report()` due to `changes` in scater parameters

Changes in version 1.3.11:

    o   added `get_ercc_anno()` function to retrieve ERCC annotation as
	 data.frame

    o   fixed `sc_detect_bc()` returning one more cell than requested

Changes in version 1.3.10:

    o   added option to use GRanges objects as annotation

    o   added option to use SAF formatted data.frame objects as annotation

    o   added support for gzipped annotation files

Changes in version 1.3.8:

    o   fix a minor bug in cell barcode demultiplexing

    o   corrected `suffix` argument in `sc_detect_bc` to `prefix`

Changes in version 1.3.7:

    o   added multithreading to `parse_align`

    o   added nthreads argument to `parse_align` and all upstream wrappers

Changes in version 1.3.6:

    o   support multiple bam file for the same sample pooling as input for
	 exon mapping

Changes in version 1.3.5:

    o   bug fix

Changes in version 1.3.4:

    o   put `distance_to_end` back.

Changes in version 1.3.2:

    o   Added gzipped output for `sc_trim_barcode()`, if output filename
	 ends with `.gz` then gzipped output will be produced.

    o   Added `get_read_str()` function for getting common read structures.

Changes in version 1.3.1:

    o   updated the `sc_exon_mappping` function so it can accept multiple
	 bam files now, together with a list of cell id or cell barcode.

Changes in version 1.1.4:

    o   improved the `sc_detect_bc` function. add white list which is a list
	 of known 10x barcode also added a new argument `number_of_cells` to
	 limit the maximum number of cell barcodes in the result.

Changes in version 1.1.0-1.1.3:

    o   fix the bugs that related to the reimplementation of the exon
	 mapping algorithm

Changes in version 1.0.9:

    o   fix the bug that might misalign the exon mapping reads

    o   support gff files from gencode or refseq

Changes in version 1.0.8:

    o   update the gene id annotation code

Changes in version 1.0.6 (2017-12-18):

    o   Now the id conversion can also be done by using the bioconductor
	 annotation package, when biomart fails to connect.

Changes in version 1.0.5 (2017-12-14):

    o   Fixed bugs in slim report and trimbarcode error message

    o   Fix incomplete error message

    o   Documentation updates, new functions and bug fixes

Changes in version 1.0.4 (2017-12-04):

    o   In `detect_outlier`, give more informative error message when some
	 cells or QC metrics have zero values.

Changes in version 1.0.3 (2017-12-03):

    o   fix a bug in `validObject`. the default value for gene id and
	 organism is set to NA

Changes in version 1.0.2 (2017-12-01):

    o   fix errors in unittest

Changes in version 1.0.1 (2017-11-28):

    o   Bug Fix: Fixed handling of colData through QC_metrics
	 (https://github.com/LuyiTian/scPipe/issues/34)

Changes in version 0.99.20 (2017-09-22):

    o   scPipe now supports SingleCellExperiment class and use it as the
	 base class

    o   add two functions `plot_demultiplex` and `plot_UMI_dup`

    o   scPipe support the offical bam tags for cell barcode and UMI

Changes in version 0.99.0 (2017-07-28):

    o   Package prepared for Bioconductor submission.