getSequenceNames() returns an array of string integers instead of the sequence names

[shihabdider]

I'm trying to retrieve the list of sequence names in the fasta file but it seems that the getSequenceNames() method just returns a list of ints (as strings) of length the number of sequences in the fasta. If I run getSequenceSizes(), the names of the sequences in the returned object keys are different (and correct), but if I use getSequenceSize(seqName) with one of the seqNames returned from getSequenceNames() the return is undefined.

seq.getSequenceNames()
[
  '0',  '1',  '2',  '3',  '4',  '5',  '6',  '7',  '8',  '9',
  '10', '11', '12', '13', '14', '15', '16', '17', '18', '19',
  '20', '21', '22', '23', '24', '25', '26', '27', '28', '29',
  '30', '31', '32', '33', '34', '35', '36', '37', '38', '39',
  '40', '41', '42', '43', '44', '45', '46', '47', '48', '49',
  '50', '51', '52', '53', '54', '55', '56', '57', '58', '59',
  '60', '61', '62', '63', '64', '65', '66', '67', '68', '69',
  '70', '71', '72', '73', '74', '75', '76', '77', '78', '79',
  '80', '81', '82', '83', '84', '85', '86', '87', '88', '89',
  '90', '91', '92', '93', '94', '95', '96', '97', '98', '99',
  ... 355 more items
]

seq.getSequenceSizes()
{
  'NC_000001.11': 248956422,
  'NT_187361.1': 175055,
  'NT_187362.1': 32032,
  'NT_187363.1': 127682,
  'NT_187364.1': 66860,
  'NT_187365.1': 40176,
  'NT_187366.1': 42210,
  'NT_187367.1': 176043,
  'NT_187368.1': 40745,
  'NT_187369.1': 41717,
  'NC_000002.12': 242193529,
  'NT_187370.1': 161471,
  'NT_187371.1': 153799,
  'NC_000003.12': 198295559,
  ...
}

seq.getSequenceSize('0')
undefined

[garrettjstevens]

It appears we have two methods that are supposed to do the same thing (or at least they have the exact same JSDoc description), but one of them doesn't work correctly. getSequenceNames() appears to not work, as you described, however getSequenceList() does work and should provide the information you're looking for.

[cmdcolin]

Thanks for catching...I propose #50 to fix (just updating the docs to refer to getSequenceList() instead of getSequenceNames())