Commit c071ae97 authored by Steffen Möller's avatar Steffen Möller
Browse files

New upstream version 2.3.1

parent 5eb60d22

.gitignore

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.vscode

build

googletest-release*

*~

AdapterRemoval.1

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.\" Man page generated from reStructuredText.

.

.TH "ADAPTERREMOVAL" "1" "Jan 22, 2019" "2.2.3" "AdapterRemoval"

.TH "ADAPTERREMOVAL" "1" "Jun 23, 2019" "2.3.0" "AdapterRemoval"

.SH NAME

AdapterRemoval \- Fast short-read adapter trimming and processing

.
@@ -254,6 +254,11 @@ Set the threshold for trimming low quality bases using \fB\-\-trimqualities\fP a 
.UNINDENT

.INDENT 0.0

.TP

.B \-\-preserve5p

If set, bases at the 5p will not be trimmed by \fB\-\-trimns\fP, \fB\-\-trimqualities\fP, and \fB\-\-trimwindows\fP\&. Collapsed reads will not be quality trimmed when this option is enabled.

.UNINDENT

.INDENT 0.0

.TP

.B \-\-minlength length

Reads shorter than this length are discarded following trimming. Defaults to 15.

.UNINDENT

CHANGES.md

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### Version 2.3.1 - 2019-06-23



 * Added --preserve5p option. This option prevents AdapterRemoval from trimming

   the 5p of reads when the --trimqualities, --trimns, and --trimwindows options

   are used. Neither end of collapsed reads are trimmed when this option is used.

 * Fixed Ns being miscounted as As when constructing consensus adapter sequences

   using --identify-adapters.





### Version 2.3.0 - 2019-03-12



 * Fixed --collapse producing slightly different result on 32 bit and 64 bit

   architectures. Courtesy of Andreas Tille.

 * Added support for output files without a basename; to create such output

   files, use an empty basename (--basename "") or a basename ending with a 

   slash (--basename path/).

 * Added support for managing file handles to allow AdapterRemoval to run

   when the the number of output files exceeds the number of file handles, e.g.

   when demultiplexing large numbers of samples.

 * Reworked demultiplexing to improve performance for many paired barcodes.





### Version 2.2.4 - 2019-02-10



  * Fixed bug in --trim5p N which would AdapterRemoval to abort if N was greater

Makefile

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@@ -65,7 +65,9 @@ PROG := AdapterRemoval 
LIBNAME  := libadapterremoval

LIBOBJS  := $(BDIR)/adapterset.o \

            $(BDIR)/alignment.o \

            $(BDIR)/alignment_tables.o \

            $(BDIR)/argparse.o \

            $(BDIR)/barcode_table.o \

            $(BDIR)/debug.o \

            $(BDIR)/demultiplex.o \

            $(BDIR)/fastq.o \
@@ -76,6 +78,7 @@ LIBOBJS := $(BDIR)/adapterset.o \ 
            $(BDIR)/main_adapter_id.o \

            $(BDIR)/main_adapter_rm.o \

            $(BDIR)/main_demultiplex.o \

            $(BDIR)/managed_writer.o \

            $(BDIR)/scheduler.o \

            $(BDIR)/strutils.o \

            $(BDIR)/threads.o \
@@ -152,9 +155,12 @@ TEST_DIR := build/tests 
TEST_OBJS := $(TEST_DIR)/main_test.o \

             $(TEST_DIR)/debug.o \

             $(TEST_DIR)/alignment.o \

             $(TEST_DIR)/alignment_tables.o \

             $(TEST_DIR)/alignment_test.o \

             $(TEST_DIR)/argparse.o \

             $(TEST_DIR)/argparse_test.o \

             $(TEST_DIR)/barcodes_test.o \

             $(TEST_DIR)/barcode_table.o \

             $(TEST_DIR)/fastq.o \

             $(TEST_DIR)/fastq_test.o \

             $(TEST_DIR)/fastq_enc.o \

README.md

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@@ -34,7 +34,7 @@ AdapterRemoval was originally published in Lindgreen 2012: 
If you have Conda [installed on your system](https://conda.io/miniconda.html):



```

 conda install -c maxibor adapterremoval2

 conda install -c bioconda adapterremoval

```



### Manual installation