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Commits : Listings

Analyzed 5 months ago. based on code collected over 3 years ago.
Dec 18, 2019 — Dec 18, 2020
Commit Message Contributor Files Modified Lines Added Lines Removed Code Location Date
Updated for version number and inclusion of tests dir.
jkbonfield
More... over 15 years ago
Fixed some bashisms and switched to make use of srcdir instead of top_srcdir/tests.
jkbonfield
More... over 15 years ago
Fixed tests to use $outdir for output directory so we can neatly tidy it up for make distclean. Without this make distcheck fails.
jkbonfield
More... over 15 years ago
First pass at a "make check" target. Currently this is centred around the newer code, specifically SRF support.
jkbonfield
More... over 15 years ago
Added extra error checking from Steven Leonard to spot duplicate read names. The new -c option also allows checking of an existing srf file without attempting to write a new index.
jkbonfield
More... over 15 years ago
Added support for SRFB_NULL_INDEX so that srf files with a blank index do not causes crashes.
jkbonfield
More... over 15 years ago
Major overhaul from Steven Leonard. It now supports a -fastq option to output fastq instead of ZTR files and optionally can use calibrated or non-calibrated confidence values too.
jkbonfield
More... over 15 years ago
Include string.h for additional prototypes (for -Wall -Wno-paranthesis compilations).
jkbonfield
More... over 15 years ago
Added two new programs from Steven Leonard.
jkbonfield
More... over 15 years ago
Made partial_decode_ztr non-static and added it, along with ztr_dup and construct_trace_name to the external header file for use in other parts of io_lib.
jkbonfield
More... over 15 years ago
Added include of io_lib_config.h for autoconf builds so that the ftello and similar functions get the correct prototypes.
jkbonfield
More... over 15 years ago
Minor speed tweaks to qshift and unqshift
jkbonfield
More... over 15 years ago
*** empty log message ***
jkbonfield
More... over 15 years ago
Fixed the LIBCURL_CHECK_CONFIG code to not believe the output from "curl-config --libs". We try -lcurl first off to see if that also works. The reason is simply that curl-config --libs typically loves to explicitly specify all the implicit dependencies, such as -lssl -lcrypto -ldl, etc. This in turn locks compiled io_lib libraries and binaries into requiring very specific version of system libraries.
jkbonfield
More... over 15 years ago
Updated 454's copyright notice (following correspondence from Jim Knight at 454) to explicitly include permission to modify and redistribute the code.
jkbonfield
More... over 15 years ago
Fixed bug reported by Robert Sanders. The fwd matrix was being written twice on paired-end runs instead of fwd+reverse.
jkbonfield
More... over 15 years ago
Removed requirement of database name being "dbname.version".
jkbonfield
More... almost 16 years ago
Overhauled the tcl objects somewhat. Contigs and sequence (more to follow) sport an "io" and a "delete" method. This comes about from the realisation that my object system doesn't really fit in with Tcl.
jkbonfield
More... almost 16 years ago
Added cache_incr/decr calls around contig_seqs_in_range2 so that the recursive nature of the function cannot push the bin out of the cache.
jkbonfield
More... almost 16 years ago
Bug fixed the new flush code. Using ARR instead of arr macro auto-extends the array for us.
jkbonfield
More... almost 16 years ago
Renamed ILLUMINA_GA_PARAMS and ILLUMINA_GA_PARAMS2 to ILLUMINA_GA_BUSTARD_PARAMS and ILLUMINA_GA_FIRECREST_PARAMS.
jkbonfield
More... almost 16 years ago
*** empty log message ***
jkbonfield
More... almost 16 years ago
Added external codes2codeset() function to turn bit-length arrays into codesets. Useful for tools that wish to use this code to use their own precomputed huffman trees.
jkbonfield
More... almost 16 years ago
Added an "edits_made" sub-command of the editor. This is used to implement a warning on editor exit to ask if changes should be saved.
jkbonfield
More... almost 16 years ago
Fixed the cache_flush code to hand over cache_items from a "derived" io to the base io struct before running cache_flush on the base.
jkbonfield
More... almost 16 years ago
Added the second .params file (Data directory).
jkbonfield
More... almost 16 years ago
Added Editor class save sub-command.
jkbonfield
More... almost 16 years ago
Minor tweaks to replace gap4 with gap5 in strings, functions and version (gap v5.00 now)
jkbonfield
More... almost 16 years ago
Made the contig editor using a child io for editing in. The save button now works.
jkbonfield
More... almost 16 years ago
Tidyup to support tgap library being part of the staden build system now.
jkbonfield
More... almost 16 years ago