fastq-tools.git
5 years agoMerge tag 'upstream/0.6' master
Don Armstrong [Tue, 17 Dec 2013 22:31:31 +0000 (14:31 -0800)]
Merge tag 'upstream/0.6'

Upstream version 0.6

5 years agoImported Upstream version 0.6 upstream
Don Armstrong [Tue, 17 Dec 2013 22:31:30 +0000 (14:31 -0800)]
Imported Upstream version 0.6

5 years agoFix linker error for fastq-sample. (fixes #4)
Daniel Jones [Wed, 19 Jun 2013 07:21:05 +0000 (00:21 -0700)]
Fix linker error for fastq-sample. (fixes #4)

5 years agoAdd missing man page (fixes #5)
Daniel Jones [Wed, 19 Jun 2013 07:07:06 +0000 (00:07 -0700)]
Add missing man page (fixes #5)

6 years agoLink against libm
Daniel Jones [Fri, 22 Feb 2013 22:19:24 +0000 (14:19 -0800)]
Link against libm

6 years agoAdd missing sys/stat.h include.
Daniel Jones [Wed, 20 Feb 2013 19:22:08 +0000 (11:22 -0800)]
Add missing sys/stat.h include.

6 years agoAdd a program to detect quality score encoding (fastq-qscale).
Daniel Jones [Fri, 14 Dec 2012 06:10:49 +0000 (22:10 -0800)]
Add a program to detect quality score encoding (fastq-qscale).

6 years agoHTML output for man pages.
Daniel Jones [Mon, 10 Dec 2012 04:22:21 +0000 (20:22 -0800)]
HTML output for man pages.

6 years agoMan page for fastq-sort. Bump version.
Daniel Jones [Sun, 9 Dec 2012 21:24:34 +0000 (13:24 -0800)]
Man page for fastq-sort. Bump version.

6 years agoSort by gc content and mean quality score, and seededing of random sort.
Daniel Jones [Sun, 9 Dec 2012 20:59:06 +0000 (12:59 -0800)]
Sort by gc content and mean quality score, and seededing of random sort.

6 years agoFix a bug causing random sort to be not so random.
Daniel Jones [Sun, 9 Dec 2012 20:05:17 +0000 (12:05 -0800)]
Fix a bug causing random sort to be not so random.

6 years agoRename hash to hash_table.
Daniel Jones [Sun, 9 Dec 2012 03:41:17 +0000 (19:41 -0800)]
Rename hash to hash_table.

6 years agoBuffer size option.
Daniel Jones [Tue, 9 Oct 2012 22:53:12 +0000 (15:53 -0700)]
Buffer size option.

6 years agoReverse sort option.
Daniel Jones [Tue, 9 Oct 2012 22:41:08 +0000 (15:41 -0700)]
Reverse sort option.

6 years agoAn essentially functional fastq-sort program.
Daniel Jones [Tue, 9 Oct 2012 22:20:04 +0000 (15:20 -0700)]
An essentially functional fastq-sort program.

6 years agoWIP on a fastq-sort program.
Daniel Jones [Tue, 9 Oct 2012 17:37:19 +0000 (10:37 -0700)]
WIP on a fastq-sort program.

6 years agoFix the weird output behavior of fastq-sample.
Daniel Jones [Tue, 9 Oct 2012 07:06:12 +0000 (00:06 -0700)]
Fix the weird output behavior of fastq-sample.

6 years agoMuch simpler faster code for parsing fastq files.
Daniel Jones [Tue, 9 Oct 2012 06:20:25 +0000 (23:20 -0700)]
Much simpler faster code for parsing fastq files.

7 years agoAn option for fastq-grep to output non-matching entries to a file (e.g. for splitting...
Daniel Jones [Mon, 12 Dec 2011 20:10:55 +0000 (12:10 -0800)]
An option for fastq-grep to output non-matching entries to a file (e.g. for splitting a fastq file)

7 years agoAdd the offset, not subtract.
Daniel Jones [Tue, 22 Nov 2011 22:50:32 +0000 (14:50 -0800)]
Add the offset, not subtract.

7 years agoRemove an extraneous printf.
Daniel Jones [Tue, 22 Nov 2011 22:48:08 +0000 (14:48 -0800)]
Remove an extraneous printf.

7 years agofastq-qualadj: Prevent getopt from choking on negative number arguments.
Daniel Jones [Tue, 22 Nov 2011 22:46:51 +0000 (14:46 -0800)]
fastq-qualadj: Prevent getopt from choking on negative number arguments.

7 years agoAdded a program to adjust quality scores by a fixed offset.
Daniel Jones [Tue, 22 Nov 2011 20:40:21 +0000 (12:40 -0800)]
Added a program to adjust quality scores by a fixed offset.

7 years agoREADME clarifications.
Daniel Jones [Fri, 18 Nov 2011 20:26:43 +0000 (12:26 -0800)]
README clarifications.

7 years agoFix inverted match option in fastq-grep.
Daniel Jones [Fri, 18 Nov 2011 19:10:00 +0000 (11:10 -0800)]
Fix inverted match option in fastq-grep.

7 years agofastq-sample: options to set the rng seed and output the complement of the sample
Daniel Jones [Wed, 26 Oct 2011 19:24:06 +0000 (12:24 -0700)]
fastq-sample: options to set the rng seed and output the complement of the sample

7 years agoA program to randomly sample reads from a fastq file.
Daniel Jones [Tue, 25 Oct 2011 20:45:51 +0000 (13:45 -0700)]
A program to randomly sample reads from a fastq file.

7 years agoAn option to let fastq-grep match read ids instead of sequence.
Daniel Jones [Tue, 25 Oct 2011 00:47:34 +0000 (17:47 -0700)]
An option to let fastq-grep match read ids instead of sequence.

7 years agoa few fixes, and a program to tabulate quality scores
Daniel Jones [Fri, 8 Jul 2011 21:59:52 +0000 (14:59 -0700)]
a few fixes, and a program to tabulate quality scores

8 years agoman pages
Daniel Jones [Thu, 7 Apr 2011 20:02:37 +0000 (13:02 -0700)]
man pages

8 years agoa little documentation
Daniel Jones [Fri, 18 Mar 2011 19:12:45 +0000 (12:12 -0700)]
a little documentation

8 years ago(limited) support for fasta
Daniel Jones [Thu, 17 Mar 2011 13:05:30 +0000 (06:05 -0700)]
(limited) support for fasta

8 years agoa program to output a nonredundant list of readss
Daniel Jones [Thu, 17 Mar 2011 12:53:12 +0000 (05:53 -0700)]
a program to output a nonredundant list of readss

8 years agoa couple fixes to smith-waterman
Daniel Caleb Jones [Thu, 3 Mar 2011 20:33:04 +0000 (12:33 -0800)]
a couple fixes to smith-waterman

8 years agoreimplemented smith-waterman
Daniel Caleb Jones [Thu, 3 Mar 2011 20:06:42 +0000 (12:06 -0800)]
reimplemented smith-waterman

8 years agoa new and improved parser
Daniel Caleb Jones [Thu, 3 Mar 2011 03:47:33 +0000 (19:47 -0800)]
a new and improved parser

8 years agoa program to print smith-waterman scores against a query sequence
Daniel Jones [Sat, 26 Feb 2011 20:00:04 +0000 (12:00 -0800)]
a program to print smith-waterman scores against a query sequence

8 years agoautotool script
quentin jones [Fri, 25 Feb 2011 23:36:01 +0000 (15:36 -0800)]
autotool script

8 years agoa program to tally kmer frequencies from fastq files
quentin jones [Fri, 25 Feb 2011 23:33:03 +0000 (15:33 -0800)]
a program to tally kmer frequencies from fastq files

8 years agofastq-grep works
quentin jones [Fri, 25 Feb 2011 22:48:23 +0000 (14:48 -0800)]
fastq-grep works

8 years agoinitial work on some useful fastq tools
quentin jones [Fri, 25 Feb 2011 20:46:17 +0000 (12:46 -0800)]
initial work on some useful fastq tools