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Commits : Listings

Analyzed about 5 hours ago. based on code collected about 5 hours ago.
Sep 18, 2024 — Sep 18, 2025
Commit Message Contributor Files Modified Lines Added Lines Removed Code Location Date
Reworked the output mechanism - there are now two output streams -- one for polishes to keep, one for polishes to discard -- and those can be attached to either stdout or a file. The only restriction is that both cannot be stdout. Either (or both) can be disabled.
Brian P. Walenz
More... over 22 years ago
Support for uniqPolishes
Brian P. Walenz
More... over 22 years ago
Minor bugfix in one of the error messages.
Brian P. Walenz
More... over 22 years ago
Utility to separate unique from non-unique polishes. A unique polish is one that is the only match for a given cDNA.
Brian P. Walenz
More... over 22 years ago
Added the -s "segregation" switch. It will segregate the matches by the scaffold id.
Brian P. Walenz
More... over 22 years ago
The driver code and Makefile extensions for "existDB" command line utility. Used for building and dumping a computed existDB database.
Brian P. Walenz
More... over 22 years ago
Added a printState() routine. Added an optional boolean to skip loading the table data, and to just load the parameters. Useful for just printing the state, but otherwise useless.
Brian P. Walenz
More... over 22 years ago
Added support of the defline configuration options in parseSNP. Added -snpdelimiter, -snpsizetag, -snppostag, and -snpoffset.
Brian P. Walenz
More... over 22 years ago
Added read of bzip2 compressed files.
Brian P. Walenz
More... over 22 years ago
Added defline parsing options - the size, position and field separator.
Brian P. Walenz
More... over 22 years ago
Added some error checking to read/write
Brian P. Walenz
More... over 22 years ago
Added support to serialize the existDB. The constructor will check if the file given to it is a serialized existDB and if so read it in. If not, it will build a new structure as before.
Brian P. Walenz
More... over 22 years ago
Added a short description of what it does, and parameterized some of the options.
Brian P. Walenz
More... over 22 years ago
Fixed a C++ new [] coupled with a free() error.
Brian P. Walenz
More... over 22 years ago
All sequences are toupper()'d before running sim4.
Brian P. Walenz
More... over 22 years ago
Fixed an off-by-two error in the global percent identity.
Brian P. Walenz
More... over 22 years ago
Added "-table" and "-stream" as aliases for -genomic and -cdna, resp.
Brian P. Walenz
More... over 22 years ago
Added include for bzero (AIX port)
Brian P. Walenz
More... over 22 years ago
Added -species rat to ESTmapper.pl and main Makefile
Brian P. Walenz
More... over 22 years ago
Added error checking around fread() and fwrite()
Brian P. Walenz
More... over 22 years ago
Fixed two problems: 1) readBucket would occasionally die with IOT trap -- it would try to read a bucket after the last, and it got a bogus number of things in the bucket. 2) dump.C wasn't reading counts with a small chckBits value correctly - it assumed that the counts would fit into four blocks (of size chckBits).
Brian P. Walenz
More... over 22 years ago
Support for merle
Brian P. Walenz
More... over 22 years ago
merle: uses the obvious array based method for counting mers. Limited to mers < 15 bp. Does not write meryl format output, just dumps the counts.
Brian P. Walenz
More... over 22 years ago
Added AROPTS for AIX build
Brian P. Walenz
More... over 22 years ago
Fixed paths for SNP parsing. Oops.
Brian P. Walenz
More... over 22 years ago
Added support for automagic parsing of SNPs
Brian P. Walenz
More... over 22 years ago
Renamed pickBestSNP to parseSNP
Brian P. Walenz
More... over 22 years ago
Renamed from pickBestSNP.c
Brian P. Walenz
More... over 22 years ago
Added a help screen.
Brian P. Walenz
More... over 22 years ago
Incorporated the mapsnp changes needed to map r26 hCV's to r27. Now using -singlecoverage 0.3 -multiplecoverage 0.3 -mincoverage 80 -minidentity 95 by default for -mapsnp. These are untested for dbSNP!
Brian P. Walenz
More... over 22 years ago