2015-10-05  Nicolas Joly  <njoly@pasteur.fr>

	* src/fqstats.c: New tool that report some basic informations
	(sequences number and base count) from FastQ files.
	* doc/fqstats.pod: Document it.
	* test/fqstats.sh: Exercize it.

2014-06-12  Nicolas Joly  <njoly@pasteur.fr>

	* src/fqconvert.c: Major rewrite to handle gzip(1) compressed
	files and better overall performance.
	* test/gzpress.sh: Exercize it.

2014-04-02  Nicolas Joly  <njoly@pasteur.fr>

	* src/fqextract.c: Major rewrite to handle gzip(1) compressed
	data.
	* test/gzpress.sh: Exercize it.

2014-04-01  Nicolas Joly  <njoly@pasteur.fr>

	* src/fqseqpair.pl, doc/fqseqpair.*: New tool that list names of
	sequence pairs given two FastQ files.
	* test/fqseqpair.sh: Exercize it.

2014-03-28  Nicolas Joly  <njoly@pasteur.fr>

	* test/gzpress.sh: New file to exercize compressed input files.

2014-03-27  Nicolas Joly  <njoly@pasteur.fr>

	* src/fqseqname.c, doc/fqseqname.*: New tool that list names of
	sequences in FastQ formatted file.
	* test/fqseqname.sh: Exercize it.

2013-11-08  Nicolas Joly  <njoly@pasteur.fr>

	* doc/fqquality.pod: Remove obsolete statement about supported
	quality models.

2013-07-17  Nicolas Joly  <njoly@pasteur.fr>

	* src/fastq.h: New "Torrent3.0+" scoring system, that show raw
	values in range 33-78. For FastQ files generated from Torrent
	Suite v3.0+ software.
	* test/fqconvert.sh: Exercize it.

	* src/fqconvert.c: New '-l' option, to list known scoring systems.
	* doc/fqconvert.pod: Adjust accordingly.
	* test/fqconvert.sh: Exercize it.

2013-06-13  Nicolas Joly  <njoly@pasteur.fr>

	* src/fqduplicate.pl: Adjust intermediate file parsing, needed to
	output full header data with CASAVA 1.8 files.

2013-05-29  Nicolas Joly  <njoly@pasteur.fr>

	* src/fqextract.c, fqlist.c: Support new FastQ header format from
	CASAVA 1.8 generated files.
	* test/fqextract.sh: Exercize it.

2013-04-29  Nicolas Joly  <njoly@pasteur.fr>

	* src/fqlist.[ch]: New FastQ entry list implementation.
	* src/fqextract.c: Use it.
	* src/seqlist.[ch]: G/C old version.

2013-03-14  Nicolas Joly  <njoly@pasteur.fr>

	* src/fqquality.c: Make it work with all FastQ scoring formats, by
	guessing quality encoding first.

2013-03-13  Nicolas Joly  <njoly@pasteur.fr>

	* src/fconvert.c: Move FastQ scoring definition from here ...
	* src/fastq.h: ... to here.

2013-03-08  Nicolas Joly  <njoly@pasteur.fr>

	* doc/fqduplicate.pod: Fix syntax.
	* doc/fqconvert.pod: Small update.

2013-03-05  Nicolas Joly  <njoly@pasteur.fr>

	* test/fastq.sh, test/fastqrw.c: New test and utility to exercize
	FastQ format.

	* src/fqduplicate.pl: Be sure to cleanup temporary files upon
	signal receipt (interrupted, killed, ...).

	* src/fqduplicate.pl: Cleanup temporary files as soon as possible.

2013-03-04  Nicolas Joly  <njoly@pasteur.fr>

	* src/fastq.c: Do not output sequence identifier in quality header
	lines anymore (to save a few bytes in storage space, and make it
	faster to proceed/parse).

	* src/fqduplicate2.c: Abort with an appropriate error message if
	output fails for some reasons.

2013-03-04  Nicolas Joly  <njoly@pasteur.fr>

	* src/fqduplicate2.c: Adjust overall quality value by summing
	ASCII codes (encoded base qualities) without any scoring
	correction.

2013-02-26  Nicolas Joly  <njoly@pasteur.fr>

	* src/fqduplicate2.c: Update usage display for new option.

2013-02-25  Nicolas Joly  <njoly@pasteur.fr>

	* src/fqduplicate2.c: Add an option to save results to file
	instead of default standard output.
	* src/fqduplicate.pl: Use it.

	* src/fastq.c: Fix long lines handling (lines that exceed internal
	read buffer).

2013-02-22  Nicolas Joly  <njoly@pasteur.fr>

	* src/fastq.[ch]: Add a new fastq_null() function that reset
	content of an existing object. And make fastq_read() use it.

2013-02-20  Nicolas Joly  <njoly@pasteur.fr>

	* src/fqduplicate.pl, doc/fqduplicate.pod: Add '-o' option to save
	output to file instead of default standard output.
	* test/fqduplicate.sh: Exercize it.

2013-02-14  Nicolas Joly  <njoly@pasteur.fr>

	* src/fqduplicate2.c: Do not assume that paired-end sequence have
	the same length.

2013-02-08  Nicolas Joly  <njoly@pasteur.fr>

	* src/fqduplicate2.c: Do not compute md5 on the whole buffer,
	restrict it to the object size.

2012-12-14  Nicolas Joly  <njoly@pasteur.fr>

	* src/fqconvert.c, src/fqconvert.pod: Adjust conversion behaviour
	to be more consistent. Output data (unmodified) even no conversion
	is needed.
	* test/fqconvert.sh: Exercize it.

2012-12-10  Nicolas Joly  <njoly@pasteur.fr>

	* test/fqconvert.sh: New file that exercize new fqconvert tool.

	* src/fqconvert.c: Fix hard-coded value which was wrong with
	recent Illumina 1.7+ addition.

2012-12-10  Nicolas Joly  <njoly@pasteur.fr>

	* src/fqconvert.c: Fix inverted overlapping logic between Illumina
	1.5+ and 1.7+.

	* doc/fqconvert.pod: Add man page source for fqconvert tool.

2012-12-05  Nicolas Joly  <njoly@pasteur.fr>

	* src/fqconvert.c: New tool that detect qualities scoring scheme,
	and convert them to Sanger score values.

2012-10-12  Nicolas Joly  <njoly@pasteur.fr>

	* src/fastq.c: Fix a nasty bug in buffer reallocation detection,
	triggered when a line was longer than the read buffer.

2012-06-11  Nicolas Joly  <njoly@pasteur.fr>

	* src/fqextract.c: Just abort with a significant message if output
	write fails. Do not loop until end of input file.

2012-03-02  Nicolas Joly  <njoly@pasteur.fr>

	* src/fqextract.c: Add `-o' option to allow saving output to
	file. Default remains unchanged (stdout).
	* test/fqextract.sh: Exercize it.
	* doc/fqextract.pod: Adjust accordingly.

2012-02-02  Nicolas Joly  <njoly@pasteur.fr>

	* First stable (1.0) version.

2012-01-26  Nicolas Joly  <njoly@pasteur.fr>

	* src/fqextract.c: Add missing `-x' option to usage.

2011-11-29  Nicolas Joly  <njoly@pasteur.fr>

	* src/fqextract.c: Be robust against fastq files which have quality
	lines starting with '@' character.
	* test/fqextract.sh: Exercize it.

2011-02-08  Nicolas Joly  <njoly@pasteur.fr>

	* src/fqextract.*: Add support for -x option, which exclude
	entries from list (extract all except list entries).
	* test/fqextract.sh: Exercize it.

2010-12-13  Nicolas Joly  <njoly@pasteur.fr>

	* configure.ac, src/fqextract.c, src/seqlist.[ch]: Get rid of
	Berkley DB 1.85 stuff to store/retrieve sequence id, which was a
	real pain under some circumstances ... and use dedicated code
	instead which is much more efficient.

2010-11-03  Nicolas Joly  <njoly@pasteur.fr>

	* First beta (0.99) version.

