ID              e4
TITLE           Long options called ambiguous abbreviation, if a prefix of another option
AFFECTS         HMMER 3.0b3 (and earlier)
FIXED_IN        -
STATUS          CLOSED
XREF            J5/116
REPORTED_BY     Maufrais Corinne <maufrais@pasteur.fr>; 27 Nov 2009
OPENED_DATE     SRE, Tue Dec  1 11:24:43 2009
CLOSED_DATE     SRE, Tue Dec  1 11:24:46 2009
DESCRIPTION     
  hmmsim --s gives
  "Failed to parse command line: Abbreviated option "--s" is ambiguous"
  because esl_getopts thinks --s is an abbreviation for --seed or --stall.
  
  get_optidx_abbrev() revised to allow exact matches to long options.
  esl_getopts unit test revised to catch this bug.
//

ID              e3
TITLE           esl-sfetch should allow simpler fetching from small files
AFFECTS         -
FIXED_IN        -
STATUS          OPEN
XREF            J4/81
REPORTED_BY     SRE
OPENED_DATE     13 Feb 2009
CLOSED_DATE     -
DESCRIPTION     
  esl-sfetch should allow simpler fetching from a small seqfile of one
  or a few sequences. It should not require an SSI index. It should allow
  a . argument to mean "from first sequence in file". (Or perhaps it should
  allow seqs to be fetched by number, as well as name.)
//
ID              e2
TITLE           esl-seqstat can't read alignment file from stdin
AFFECTS         -
FIXED_IN        -
STATUS          CLOSED
XREF            J4/84
REPORTED_BY     SRE
OPENED_DATE     16 Feb 2009
CLOSED_DATE     16 Feb 2009
DESCRIPTION     
  sqfile_open tries to guess file format; then when msafile_open is called
  in GuessAlphabet, stdin is already feof(). Using current design, MSA can't
  be read sequentially (through sqio interface) unless format is known.
  SQFILE has a recording buffer mechanism, but it only works in sqio proper,
  not through interface to esl_msa. Added e2.sh to test for the bug.
//
ID              e1
TITLE           esl-alistat fails to read Pfam seed in MUL format
AFFECTS         -
FIXED_IN        -
STATUS          CLOSED
XREF            J4/81; J4/93
REPORTED_BY     Rob Finn
OPENED_DATE     13 Feb 2009
CLOSED_DATE     13 Feb 2009
DESCRIPTION     
  SELEX/MUL format parser was present, but not hooked up to anything.
  
  Added --informat to several esl miniapps, to allow --informat selex.
//
#
# Started Easel BUGTRAX file: SRE, Tue Dec  1 11:08:31 2009
# xref J5/116