skewer Files

=== Release Notes of "skewer" ===
version 0.2.2, April 4, 2016
1. fixed a bug introduced in version 0.2.1 which wrongly caches some trimming locations

version 0.2.1, February 26, 2016
1. support paired-reads with different read-lengths. (Thanks to Dr. Hirofumi Nakaoka) 
2. fixed a bug which causes segmentation fault and memory leakage induced in version 0.2.0 by merging source-codes via GIT repository

version 0.2.0, February 11, 2016
1. fixed a bug of 3'-end hard-clipping under amplicon mode
2. added two parameter options for outputting masked and excluded files. (Thanks to jdidion)

version 0.1.127, August 5, 2015
1. fixed a bug in detecting 5' end indels under amplicon mode
2. add an option for hard clipping off the 3' tailing bases

version 0.1.126, June 22, 2015
1. fixed a bug introduced by version 0.1.125, which causes segmentation fault in Mate-pair mode. (Thanks to Anthony Bellantuono)

version 0.1.125, May 12, 2015
1. enable to produce QIIME-compatible files for microbial analysis
2. user manual
3. fixed a small bug related to TAIL trimming (Thanks to Fabien PICHON)

version 0.1.124, March 9, 2015
1. support OS X (Thanks to Peter Wilkinson)

version 0.1.123, January 16, 2015
1. fixed a small bug introduced by version 122, which fails in processing single end reads

version 0.1.122, January 6, 2015
1. now support hard clipping after demultiplexing
2. fixed bugs related to calculating demultiplexing statistics
3. provide options for specifying valid adapter pairs

version 0.1.120, September 27, 2014
1. support the trimming mode for amplicon pair reads (bidirectional 5' trimming)
2. support the barcode-only option to facilitate amplicon demultiplexing
3. for mate-pair reads, provide an option for redistributing reads based on junction information

version 0.1.118, August 25, 2014
1. fixed a bug related to calculating LMP statistics
2. supported redirection of result to a directory by specifying -o with a slash-ending base name

version 0.1.117, July 12, 2014
1. fixed a bug related to demultiplexing (Thanks to Laurent MANCHON)
2. fixed a bug related to end quality trimming (Thanks to Dr. Florian Battke)
3. obsolete negative value for minimum read length allowed after trimming;
   empty reads can be kept by specifying "-l 0"

version 0.1.114, March 20, 2014
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1. supported extension of mate-pair reads via overlapping detection
2. supported 3' end quality trimming

version 0.1.112, March 5, 2014
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1. supported Nextera Long Mate Pair (LMP) adapter trimming
2. fixed a bug associated with FASTQ format auto detection
3. added option for trimming modes (HEAD, ANY, TAIL)

version 0.1.109, February 19, 2014
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1. input from STDIN by default
2. automatically calculate -k parameter

version 0.1.104, Junuary 14, 2014
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1. fixed a bug related to clearing bits beyond 32 bits
2. added bit operations to reach O(kn) worst time complexity

version 0.1.99, November 27, 2013
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1. fixed a deadlock in multi-threading
2. support input from STDIN, output to STDOUT; support compressing output

version 0.1.88, October 16, 2013
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1. fixed a bug of memory leak
2. support barcode demultiplexing

version 0.1.76, September 26, 2013
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First public release