Activity for SIBsim4

  • Christian Iseli committed [0b24f8]

    cleanup after cvs2git import

  • chris <> committed [8c087a]

    Imported sim4 sources

  • cvs <> committed [a6f32e]

    Added three new options: I, Y, and Z.

  • clottaz <> committed [2ef692]

    changed resolving overlaps for non-canonical splice sites

  • clottaz <> committed [8fba7f]

    non-canonical splice sites recognition

  • cvs <> committed [ae4c49]

    Fixed typo in sim4.init.c. Removed dependencies in Makefile.

  • clottaz <> committed [326fb3]

    cosmetics

  • clottaz <> committed [89e7a5]

    fixed the wobble bug

  • clottaz <> committed [ca9d22]

    fixed the problem of wrong types

  • clottaz <> committed [d3f773]

    added scoring for splice sites

  • clottaz <> committed [c44e64]

    added scoring of splice sites

  • cvs <> committed [a1ac8a]

    Change format of splice junction quality output.

  • chris <> committed [7635a4]

    Sim4 assumed an upper limit of 200 exons. Hopefully, this is now fixed.

  • cvs <> committed [7ba019]

    Reduce intron penalty.

  • cvs <> committed [0cb43d]

    Merged changes from sim4 release 2002-03-03

  • cvs <> committed [64f2cf]

    More merging from sim4 release 2002-03-03

  • cvs <> committed [ae9c1f]

    Start work on sim4b1.c; only cleanups here.

  • cvs <> committed [38fdf9]

    sim4b1.c: use qsort, remove couple global vars, remove couple functions.

  • cvs <> committed [577b34]

    Use a different (simpler) MSP linking technique.

  • cvs <> committed [71b7f5]

    Fix bug in MSP linking...

  • cvs <> committed [ee39ec]

    A bit more overlap tolerance in link_msps.

  • cvs <> committed [d29cd1]

    Add combine_msps.

  • cvs <> committed [16b842]

    Fix bug in combine_msps.

  • cvs <> committed [5432ae]

    Fix overlap bugs in combine_msps.

  • cvs <> committed [eda08b]

    Fix more overlap bugs in combine_msps.

  • cvs <> committed [bfee25]

    Fix initialization problem in link_msps.

  • cvs <> committed [364ba5]

    Started cleanup by removing EST_GEN stuff.

  • chris <> committed [8f9a5f]

    Remove unused AUXUTILS and STATS stuff.

  • chris <> committed [e29e8e]

    Remove PipMaker stuff.

  • chris <> committed [443548]

    Removed useless VERSION file.

  • cvs <> committed [f07ccd]

    Remove N option and cleanup local variables mess.

  • cvs <> committed [678c22]

    Remove a bunch of useless misc functions. Use xmalloc and friends.

  • cvs <> committed [83d24f]

    Dispose of relink.

  • chris <> committed [1a1d60]

    Fix usage message.

  • cvs <> committed [9b4cdb]

    Remove Xtend1.c Xtend1.h, and update fatal().

  • cvs <> committed [12fb09]

    Cleanup bld_table +1 mess. Harmonize encoding. Add debug output.

  • cvs <> committed [5ec154]

    Cleanup search() function.

  • cvs <> committed [ef197b]

    Cleanup exon_cores() function.

  • cvs <> committed [06b987]

    Cleanup DEBUG printout.

  • cvs <> committed [373fa6]

    Remove (seemingly) useless stats stuff.

  • cvs <> committed [3494b3]

    Fix exon merging.

  • cvs <> committed [894e9d]

    Kill is_DNA. Move add_word() to inline.

  • chris <> committed [a30706]

    Use new file reading stuff, and clean up junk.

  • chris <> committed [6fc8f8]

    Forgot to remove seq_read.c.

  • chris <> committed [249fd6]

    Use tsearch and friends instead of lists in hash table.

  • chris <> committed [dabb31]

    Fix a few leaks.

  • cvs <> committed [47553a]

    Cleanup, and localize some variables.

  • cvs <> committed [341649]

    Remove unused dist parameter.

  • cvs <> committed [dc5b4a]

    Add debugging stuff.

  • cvs <> committed [dd1f28]

    Some work on call to extend_bw().

  • cvs <> committed [6b3da1]

    Handle case of extend_fw().

  • cvs <> committed [76e6b0]

    Remove unused stuff in sim4.h.

  • cvs <> committed [47d086]

    Msp_ptr -> msp_p_t.

  • cvs <> committed [a32594]

    Generalized collection type.

  • cvs <> committed [76e6b0]

    Remove unused stuff in sim4.h.

  • chris <> committed [71f4a6]

    Fix exon freeing problem.

  • chris <> committed [f8e458]

    Use exon collection instead of list. Misc cleanups.

  • cvs <> committed [94cea0]

    A bit more debug output.

  • cvs <> committed [fe09e1]

    Fix stupid missing sizeof(type) multiplier in some memmove.

  • chris <> committed [05e2de]

    Use getopt to parse args. Add locale setting.

  • chris <> committed [9fdef7]

    Kill argv.[ch].

  • chris <> committed [d02940]

    Fix remaining fixed argv usage.

  • chris <> committed [c75f6a]

    Change handling of polyA tails. No polyA report printed yet.

  • chris <> committed [fdc98a]

    Minor cleanup on IA64.

  • chris <> committed [847551]

    Remove exit(1) on some input.

  • chris <> committed [1a9e11]

    Provide dummy tdestroy when there is no glibc.

  • chris <> committed [c8b20f]

    Better exon merging. Fix output for large DNA. Unsigned nitpicking. Trailing spaces nitpicking.

  • chris <> committed [4638ee]

    Do not create exons longer than the sequences.

  • chris <> committed [df4a1c]

    Fix bug introduced in revision 1.56 of sim4b1.c.

  • chris <> committed [2fd998]

    Output polyA info.

  • chris <> committed [b284e5]

    Add mcheck() and mtrace() in DEBUG mode.

  • chris <> committed [fffe3a]

    Fix exon number bug in sim4b1.c. Fix error messages.

  • chris <> committed [48d9bf]

    Changed sort order in msp_compare, to prepare for multi-hits.

  • chris <> committed [86fdb4]

    Start changes to allow duplicated genes resolution. Fix edit_script types...

  • chris <> committed [15d774]

    Fix uninitialized variable.

  • chris <> committed [6d0077]

    Fix decrement typo (bug).

  • chris <> committed [52a72d]

    Prepare SIBsim4 package.

  • root <> committed [cfdb73]

    initial checkin

  • chris <> committed [3583d0]

    Remove unused enum is sim4.h.

  • chris <> committed [8e799f]

    Completed duplicated genes detection.

  • chris <> committed [3f1a0a]

    Started duplicated gene detection.

  • chris <> committed [abe985]

    Fix thinko in length calculation.

  • chris <> committed [4168c6]

    Fix stupid variable name overlap.

  • chris <> committed [8195c0]

    Fix off by 1 in seq header setup.

  • chris <> committed [d5294a]

    Add missing check when looking for more tail exons.

  • chris <> committed [229ea9]

    Fix parameter swap in call to exon_cores().

  • chris <> committed [b379c3]

    Add missing check when looking for more head exons.

  • chris <> committed [a445dc]

    Remove useless error message.

  • chris <> committed [7b7351]

    Print only the better matches.

  • chris <> committed [ab5070]

    Properly handle unsigned comparison.

  • c4chris <> committed [90ffdd]

    Add man page. Fix usage info.

  • c4chris <> committed [c40b95]

    This commit was manufactured by cvs2svn to create tag 'SIBsim4_0_5'.

  • c4chris <> committed [e2ebb0]

    Create htdocs module.

  • c4chris <> committed [0d5561]

    This commit was manufactured by cvs2svn to create tag 'start'.

  • c4chris <> committed [bb6b6e]

    Add links to manpage and changes.

  • c4chris <> committed [251ed3]

    Add initial release info.

  • c4chris <> committed [4cdc9a]

    Replace col_t with collec_t, as col_t is used in AIX.

  • c4chris <> committed [6e86bd]

    Cleanup leftover memory alloc stuff.

  • c4chris <> committed [3da0af]

    Instrument for a bit more debugging output.

  • c4chris <> committed [3299d1]

    Cleanup.

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