| fe0206d | Indraniel Das | 30 June 2011, 22:50:58 UTC | + gmt-web fix macports label markdown bug | 30 June 2011, 22:50:58 UTC |
| 3bef250 | Indraniel Das | 30 June 2011, 22:29:11 UTC | + gmt-web icon addition - addition of the 16x16 pixel icon | 30 June 2011, 22:29:11 UTC |
| 3f425b9 | Indraniel Das | 30 June 2011, 21:21:47 UTC | + gmt-web install page formatting fix - get the code text formatted correctly for the alternative installation section. | 30 June 2011, 21:21:47 UTC |
| c41231f | Indraniel Das | 30 June 2011, 21:03:46 UTC | + gmt-web installation page update - the code block for the installation sub-section correctly formatted | 30 June 2011, 21:03:46 UTC |
| 5593d60 | Indraniel Das | 30 June 2011, 20:55:46 UTC | + minor formatting fixes - get the bullet list to format correctly. | 30 June 2011, 20:55:46 UTC |
| c386a7c | Indraniel Das | 30 June 2011, 20:33:30 UTC | + more gmt-web documentation fixes - ensure that all github links go to the github page - adjust the reference documenation link page on the index page - place a link to the latest GPL license | 30 June 2011, 20:33:30 UTC |
| 7d188bb | Indraniel Das | 30 June 2011, 20:21:17 UTC | + gmt-web documentation page update - further indent the body of the SYNOPSIS section to get the <pre> formatting syntax | 30 June 2011, 20:21:17 UTC |
| 7a40e00 | Indraniel Das | 30 June 2011, 20:13:52 UTC | + further flushing out the gmt-web based documentation Addition of the Documentation and Install pages. | 30 June 2011, 20:13:52 UTC |
| c2d9b6e | Indraniel Das | 21 June 2011, 19:13:29 UTC | + addition of the gmt website icon image | 21 June 2011, 19:13:29 UTC |
| 1ac02e5 | Indraniel Das | 21 June 2011, 18:01:08 UTC | + gmt-web configuration file rename | 21 June 2011, 18:01:08 UTC |
| 04d5d73 | Indraniel Das | 21 June 2011, 17:42:45 UTC | + initial gmt-website setup - initial Overview Documentation | 21 June 2011, 17:42:45 UTC |
| 14d48a1 | Indraniel Das | 16 May 2011, 12:35:20 UTC | + addition of wiki page reference - Adjust documentation to point to relevant wiki page - minor formatting changes | 16 May 2011, 12:35:20 UTC |
| 85d330e | Indraniel Das | 16 May 2011, 12:14:24 UTC | + addition of the example "trimmer" script | 16 May 2011, 12:14:24 UTC |
| 15c1b2b | Indraniel Das | 16 March 2011, 14:46:04 UTC | + add FASTQ/FASTA descriptions in README - add Wikipedia links describing FASTQ/FASA format files | 16 March 2011, 14:46:04 UTC |
| 684f015 | Indraniel Das | 16 March 2011, 14:27:54 UTC | + adjust version (0.4.2) -- help message re-arrangements - adjust the help message - mention about FASTA and FASTQ files as input - move the -a option closer to the -v option as they are somewhat related. | 16 March 2011, 14:27:54 UTC |
| 5143077 | Indraniel Das | 15 March 2011, 23:08:00 UTC | + more minor README language fixes - update the date on the README - be more explicit on the selected "report" and "read data" terms | 15 March 2011, 23:08:00 UTC |
| 524ff5d | Indraniel Das | 15 March 2011, 22:58:48 UTC | + README modification be more explicit about the piping/streaming/reading from stdin ability of fqgrep. | 15 March 2011, 22:58:48 UTC |
| 0779f23 | Indraniel Das | 15 March 2011, 22:46:48 UTC | + grammar and formatting fixes in README - usage of the term 'fqgrep' in the first sentence, and an application of 'fmt' on the first paragraph. | 15 March 2011, 22:46:48 UTC |
| de5e313 | Indraniel Das | 15 March 2011, 22:31:58 UTC | + minor README language fixes - mention about using the -a and -r option for post-processing the data - mention about examples in the fqgrep-trim.pl description/documentation | 15 March 2011, 22:31:58 UTC |
| 7d94e3f | Indraniel Das | 15 March 2011, 22:21:49 UTC | + remove commented out logic in the trim script - remove the unused portion of the code that was attempting to construct a read mismatch count histogram. This was not really needed as one could derive the stats from the read count histogram (rch) output file. | 15 March 2011, 22:21:49 UTC |
| d17cc53 | Indraniel Das | 15 March 2011, 22:20:02 UTC | + enable 'fqgrep -a' option usage in the trim script - changes to enable '-a' option usage. This makes the script a bit more memory efficient - update the version to '0.2.0' | 15 March 2011, 22:20:02 UTC |
| 859d202 | Indraniel Das | 15 March 2011, 20:22:41 UTC | + mention illustrative purposes of the trim script | 15 March 2011, 20:22:41 UTC |
| 0579d06 | Indraniel Das | 15 March 2011, 20:21:16 UTC | + minor refactoring on the fqgrep-trim.pl script - addition of a --version option - movement of all the input validation checks into its own subroutine - display the elapsed time on dumping out the stats | 15 March 2011, 20:21:16 UTC |
| ff1310c | Indraniel Das | 14 March 2011, 21:52:56 UTC | + more README cleanup - mentioning of /usr/local/bin and removal of an extraneous line | 14 March 2011, 21:52:56 UTC |
| 50ef206 | Indraniel Das | 14 March 2011, 21:35:32 UTC | + update README - account for the -v, -V, -l option changes done in the prior commit. | 14 March 2011, 21:35:32 UTC |
| 3af7456 | Indraniel Das | 14 March 2011, 21:24:12 UTC | + adjust version (0.4.1) and options to be more like 'grep' - the invert records option in grep is -v not -l make fqgrep's -v option (version info) to be the invert match make a -V (capital V) to report version information - adjust formatting in version message -- remove extra whitespace | 14 March 2011, 21:24:12 UTC |
| bd8a054 | Indraniel Das | 14 March 2011, 00:46:58 UTC | + update the program version to 0.4.0 | 14 March 2011, 00:46:58 UTC |
| 5f62500 | Indraniel Das | 09 March 2011, 21:47:20 UTC | + README updates - mention the addition of the new '-l' and '-a' options. - place a comment about the streaming (ability to read from STDIN) functionality. | 09 March 2011, 21:47:20 UTC |
| 7a50ff5 | Indraniel Das | 09 March 2011, 21:20:32 UTC | + addition of a '-a' option -- show all matches Show all records irregardless of match status. Useful in conjunction with the -r option when one would like to do further custom post-processing on the data. | 09 March 2011, 21:20:32 UTC |
| d593012 | Indraniel Das | 04 March 2011, 20:18:14 UTC | + help formatting change (on -l / invert match option) Split the help description of the -l option into two lines. For the ease of reading in narrow terminals. | 04 March 2011, 20:18:14 UTC |
| 231f651 | Indraniel Das | 02 March 2011, 06:12:34 UTC | + addition of an invert match option (-l) Show only sequences that DO NOT match the pattern. Mimic a regular grep feature... Regular grep had a '-L' option that would: "suppress the normal output; and instead print the name of each input file from which no output would normally have been printed". | 02 March 2011, 06:12:34 UTC |
| e76bceb | Indraniel Das | 02 March 2011, 05:35:37 UTC | + be able to read from stdin This is a first-pass approach. The stdin will implicitly accept an input of the FASTQ or FASTA format. Any other format may give undesired and unknown behavior. | 02 March 2011, 05:35:37 UTC |
| 63435d9 | Indraniel Das | 16 February 2011, 18:05:08 UTC | + update acknowledgement section | 16 February 2011, 18:05:08 UTC |
| fae2dd5 | Indraniel Das | 11 February 2011, 15:18:41 UTC | + change file permissions on fqgrep-trim.pl Make the script executable. | 11 February 2011, 15:20:12 UTC |
| 1b8e013 | Indraniel Das | 11 February 2011, 15:16:09 UTC | + minor README changes - move the 'Path::Class' installation notes into the PREREQUISITES section - mention of 'sudo' in the Ubuntu installation - note the usage of POSIX styled regular expressions | 11 February 2011, 15:20:12 UTC |
| 5e0f446 | Indraniel Das | 02 February 2011, 20:19:54 UTC | + documentation fixes - Addition of a couple examples in the EXAMPLE section - Ensure that the default option values appear at the end and are bold. | 02 February 2011, 20:19:54 UTC |
| b95ea3b | Indraniel Das | 02 February 2011, 19:45:13 UTC | + README additions - rearrangement of the text regarding the approximate searching strategy - mention of TRE usage in R | 02 February 2011, 19:45:13 UTC |
| f79baa8 | Indraniel Das | 02 February 2011, 19:39:52 UTC | + correctly dump the untrimmed reads into the desired input format Before, the untrimmed reads were only getting dumped into a FASTQ format. | 02 February 2011, 19:39:52 UTC |
| b4a4305 | Indraniel Das | 02 February 2011, 06:09:11 UTC | + email format description changes | 02 February 2011, 06:09:26 UTC |
| eb79934 | Indraniel Das | 02 February 2011, 06:08:38 UTC | + mention fqgrep-trim.pl in the README | 02 February 2011, 06:08:38 UTC |
| 1271e8d | Indraniel Das | 02 February 2011, 06:06:58 UTC | + module / options / documentation sync and cleanup | 02 February 2011, 06:07:48 UTC |
| 14a4bf4 | Indraniel Das | 02 February 2011, 05:03:47 UTC | + bugfixes ensure that the correct hash key is being used | 02 February 2011, 05:03:47 UTC |
| 2ba29d2 | Indraniel Das | 02 February 2011, 05:02:37 UTC | + refactoring place the input file type assessment into its own subroutine | 02 February 2011, 05:03:07 UTC |
| 2f7e03d | Indraniel Das | 02 February 2011, 04:56:45 UTC | + adjust output statistics tables - ensure that the output file names were consistent with the documentation and code - removed unused file names (the overall_count_file) - adjust subroutine input params accordingly - adjust how the table columns were being presented = read_length_histogram_table (rlh) * has 3 columns joined into one large table 'Mismatch', 'Read Length', 'Read Count' Before there were subtables with 2 columns per mismatch level = read_count_histogram_table (rch) * has only 4 columns: 'MismatchThreshold', 'TotalFilteredReads', 'Trimmed', 'Omitted', 'TotalReads' | 02 February 2011, 04:56:45 UTC |
| 5ce7aa3 | Indraniel Das | 02 February 2011, 04:51:58 UTC | + remove usage of the mismatch_count_histogram data This was a redundant set of statistics that can be derived from the other output statistics files. | 02 February 2011, 04:51:58 UTC |
| 5a144a3 | Indraniel Das | 01 February 2011, 23:27:56 UTC | + proper output filename descriptions in documentation | 01 February 2011, 23:27:56 UTC |
| 9052e27 | Indraniel Das | 01 February 2011, 23:21:37 UTC | + application of fmt on sections of the documentation | 01 February 2011, 23:21:37 UTC |
| d384fd2 | Indraniel Das | 01 February 2011, 23:19:54 UTC | + adjust file name suffixes for output stat files the read-count-histogram file output should have a 'rch' suffix appended the read-length-histogram file output should have a 'rlh' suffix appended be also consistent in the documentation too. | 01 February 2011, 23:19:54 UTC |
| 0f71134 | Indraniel Das | 01 February 2011, 23:19:09 UTC | + ensure the trim option takes an argument | 01 February 2011, 23:19:09 UTC |
| 8d0ff0a | Indraniel Das | 01 February 2011, 23:01:06 UTC | + standardize the options documentation section - usage of single quotes for the available option values - usage of the 'or' clause instead of '|' | 01 February 2011, 23:01:06 UTC |
| 1a00c43 | Indraniel Das | 01 February 2011, 23:00:06 UTC | + set verbose level 1 for Pod::Usage - remove out the extra unncessary options summary in the POD. | 01 February 2011, 23:00:06 UTC |
| cbdb5f8 | Indraniel Das | 01 February 2011, 22:56:00 UTC | + addition of a --help option via Pod::Usage | 01 February 2011, 22:56:00 UTC |
| 11a9209 | Indraniel Das | 01 February 2011, 22:55:24 UTC | + convert read-mismatch-count-histogram to read-count-histogram | 01 February 2011, 22:55:24 UTC |
| a65b063 | Indraniel Das | 01 February 2011, 21:49:26 UTC | + NOTES section grammar fix and reformatting + 'consequence' => 'the consequence' | 01 February 2011, 21:49:26 UTC |
| c2679d5 | Indraniel Das | 01 February 2011, 20:39:00 UTC | + documentation refinements - application of 'par' formatting to certain sections to ensure 80 character widths. - refinement of the language in the NOTES section. | 01 February 2011, 20:39:00 UTC |
| 599497b | Indraniel Das | 01 February 2011, 06:00:47 UTC | + refactor of the fqgrep-trim.pl script - ability to work on 'left' or 'right' adaptor trimming - ability to input and output FASTA or FASTQ files - adjustment of options and documentation - ability to work on /usr/bin/env perl - addition of a GPL license - general cleanup of extraneous logic and documentation | 01 February 2011, 06:02:40 UTC |
| 50b8a48 | Indraniel Das | 01 February 2011, 05:56:30 UTC | + refactor the README for a more general audience | 01 February 2011, 05:56:30 UTC |
| e3465fc | Indraniel Das | 29 January 2011, 21:41:52 UTC | + remove extraneous gnuplot directive file | 29 January 2011, 21:41:52 UTC |
| 98dabb2 | Indraniel Das | 09 January 2011, 23:51:51 UTC | + addition of license information to fqgrep | 10 January 2011, 04:29:01 UTC |
| 5568e8d | Indraniel Das | 09 January 2011, 23:32:37 UTC | + remove unused bitap algorithm files - the libtre library (http://laurikari.net/tre/) is the desired library to use for fqgrep. The other explored alternatives (bitap.c, from wikipedia) and (libbitap, from http://rational.co.za/libbitap) are not being used currently anymore. | 10 January 2011, 04:29:01 UTC |
| 9d965af | Indraniel Das | 10 January 2011, 01:07:25 UTC | + adjust the Makefile to work on other plaforms - added the following PHONY targets: macports genome clean-genome * general 'make' - should work on general linux and unix systems all libraries are loaded dynamically * macports - for the Mac OS X installation, designed if the tre library was installed via macports (http://www.macports.org) * genome / clean-genome - for installation at the Genome Center at Washington University. The external libraries (libtre, libz) are statically complied into the final executable). To account for the multiple linux images currently available at the Center. If use 'make genome', then use 'make clean-genome' for the 'make clean'ing process. | 10 January 2011, 01:15:45 UTC |
| 80f377a | Indraniel Das | 06 January 2011, 15:28:14 UTC | + addition of author information | 06 January 2011, 15:28:14 UTC |
| ea18b7f | Indraniel Das | 03 January 2011, 18:27:11 UTC | + input error checking cleanup Now that the TRE regex engine is being used. The following error check : ensure the number of max_mismatches does not exceed the search pattern length should not be enforced, as one could make a regex that is short but could have a mismatch value applied to it that is much longer than the regex string itself. | 03 January 2011, 18:27:11 UTC |
| 0b1581f | Indraniel Das | 01 December 2010, 21:32:26 UTC | + fix copy-n-paste documentation section header typo | 01 December 2010, 21:32:26 UTC |
| f3b9ed9 | Indraniel Das | 01 December 2010, 20:31:20 UTC | + addition of example trimming and plotting scripts | 01 December 2010, 20:31:20 UTC |
| 91c9354 | Indraniel Das | 06 November 2010, 05:36:07 UTC | + removal of extraneous newline in report stats | 06 November 2010, 05:36:07 UTC |
| 02e3c2e | Indraniel Das | 05 November 2010, 08:53:18 UTC | + adjust help message - note type of input where input argument parameters are required - adjust the order of the placement of the -s, -i, -d, -S, -I, -D options in the help message. Make it consistent. | 05 November 2010, 08:53:18 UTC |
| ba3e3db | Indraniel Das | 03 November 2010, 09:02:52 UTC | + addition of 'match string' column in stat report | 03 November 2010, 09:02:52 UTC |
| 9d4d8a6 | Indraniel Das | 03 November 2010, 08:43:53 UTC | + addition of threshold options - be able to independently control the maximum threshold of allowable insertions, deletions, and substitutions in approximate pattern search - with these new options (-s, -i, -d) the older option definitions (-s and -d) had to be remapped to something new: -s => -r -d => -b | 03 November 2010, 08:43:53 UTC |
| de256d4 | Indraniel Das | 01 November 2010, 04:24:57 UTC | + allow for static linking when making fqgrep - not all workstations have either the libtre library installed, or have its latest version. To get around this issue for the moment, so that most people can try it out, statically compile it. | 01 November 2010, 04:24:57 UTC |
| 5f23e34 | Indraniel Das | 01 November 2010, 02:25:36 UTC | + addition of options to the tre-test program - make it similar to fqgrep in being able to adjust the mismatch, and cost parameters. | 01 November 2010, 02:25:36 UTC |
| 5c31b86 | Indraniel Das | 01 November 2010, 02:25:13 UTC | + printout a header in the detail stats report | 01 November 2010, 02:25:13 UTC |
| c291d4d | Indraniel Das | 31 October 2010, 19:14:11 UTC | + highlight calculation adjustments & help formatting - directly use match start & end position information when making the highlighted sequence. (For some reason the pointer arithmetic on the strings was not working in the new tre engine version) - we can now output files of various types (FASTQ, FASTA, tsv, csv reports, etc.). Omitted the usage of "fastq" in the output file option help description. | 31 October 2010, 19:14:11 UTC |
| 18db513 | Indraniel Das | 31 October 2010, 18:16:02 UTC | + a very first pass at using the tre regexp engine | 31 October 2010, 18:16:02 UTC |
| 59cb91b | Indraniel Das | 30 October 2010, 23:18:23 UTC | + a test of using the libtre library This is just seeing its basic approximate string matching usage. | 30 October 2010, 23:18:23 UTC |
| 9a1bcbf | Indraniel Das | 26 October 2010, 04:02:25 UTC | + addition of the libbitap source code files (*.c, *.h) | 26 October 2010, 04:02:25 UTC |
| f148f32 | Indraniel Das | 25 October 2010, 05:51:36 UTC | + first-pass attempt to use the libbitap library - replace the wikipedia bitap implementation with libbitap (http://rational.co.za/libbitap) libbitap handles the cases for insertions, deletions, and substitutions unlike the wikipedia version (which only dealt with substitutions). libbitap also some limited amounts of regular expression syntax. Although its usage is not well documented. | 25 October 2010, 05:52:45 UTC |
| 6f99fcf | Indraniel Das | 25 October 2010, 00:10:19 UTC | + substitute usage of strndup with stringn_duplicate - for UNIX (and C) portability reasons | 25 October 2010, 00:10:19 UTC |
| cc5fb79 | Indraniel Das | 11 October 2010, 17:20:02 UTC | + bitap algorithm pattern limit adjustment - parameterize the pattern length limit applied to the current implemented version of the bitap algorithm. - increase the limit from 31 characters to 64 characters. | 11 October 2010, 17:20:02 UTC |
| 7826354 | Indraniel Das | 11 October 2010, 17:13:14 UTC | + add a "INSTALLATION" section in the README | 11 October 2010, 17:13:14 UTC |
| 668b054 | Indraniel Das | 11 October 2010, 01:36:16 UTC | + initial import This is a quick first-pass implementation of a FASTQ sequence grepper tool. It is basically a stitch of the code mentioned in the README. | 11 October 2010, 01:57:30 UTC |
