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Changelog
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Changelog
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2018.02.09
*fixed a bug where partial (but perfect match) adapters could be missed when they were right at the end of a read
*added some rudimentary unit tests
2018.02.07
*improved a warning message
*fixed a command line parsing bug where `-a` would not trigger (long form --aggressive still worked)
2017.10.22
*removed the mergeReads binary (see seqtk for equivalent functionality)
*deprecated joinReads functionality
2017.05.27
*will now discard read pairs if one read has length < minoverlap (previously was minlength)
2017.05.26
*added a check to make sure R1/R2 files have same number of lines
2017.04.18
*added --aggressive mode for more thorough adapter search
*improved speed of hamming distance calculations
2017.04.17
*added smith-waterman routine for adapter detection - still needs improvement
*added a build script for E.coli MG1655 "make ecmg"
2017.04.08
*improved detection of reads where two copies of the Nextera junction adapter are present
2017.03.28
*better error reporting for malformed reads
2016.04.10
*added --stdout-mp and --stdout-un functionality
*changed the --norc flag to --rf
2016.03.27
*fixed a bug that occurs when comment field is empty issue #17
2016.02.27
*fixed issue #15
*removed BOOST dependencies
2015.08.13
*makefile/versioning tweaks
*added some more examples
2015.05.26
*minor bugfix concerning --justmp and external adapters
2015.05.22
*fixed a problem with header passing when reads were not in Illumina format (eg. ENA)
*added --ignorePF flag
2015.05.21
*added --stdout flag
*program output now prints to stderr rather than stdout
2014.10.17
*added some code to trim _external_ adapters from unknown libraries (should be very rare)
*added git hash to the version number
2014.10.15
*v0.2.0 results for paper resubmission
*a number of tweaks/fixes to adapter trimming logic to improve accuracy
*added a --justmp flag so only mp libraries are produced
2014.08.29
*fixed a bug in --preserve-mp
*tweaks to --joinreads (now performing better on 2x251 libraries)
2014.08.28
*fixed a bug in --joinreads
2014.08.13
*renamed example files to match documentation
2014.08.06
*added handling for fastqs with varying read lengths
*better I/O checking
*better handling of reads with large numbers of Ns
2014.08.05
*initial commit