BugsclonotypeRhttp://clonotyper.branchable.com/Bugs/clonotypeRikiwiki2015-03-19T04:13:00ZYassai ID should have no codon ID in absence of non-templated codons.http://clonotyper.branchable.com/Bugs/Yassai_ID_should_have_no_codon_ID_in_absence_of_non-templated_codons./2015-03-19T04:13:00Z2015-03-19T04:13:00Z
<pre>
> yassai_identifier(c(V="TRAV14N-1", J="TRAJ56", dna="GCAGCTACTGGAGGCAATAATAAGCTGACT", pep="AATGGNNKLT"))
[1] "aa.1A14N1A56L10"
</pre>
<p>Should be <code>aa.A14N1A56L10</code>.</p>
Use basename case-insensitivelyhttp://clonotyper.branchable.com/Bugs/Use_basename_case-insensitively/2014-06-04T22:38:29Z2014-06-04T22:38:29Z
<p>Problem:</p>
<pre><code>$ basename foo.fastq .fastq
foo
$ basename foo.FASTQ .fastq
foo.FASTQ
</code></pre>
clonotypeR detect should test the existence of the FASTQ file.http://clonotyper.branchable.com/Bugs/clonotypeR_detect_should_test_the_existence_of_the_FASTQ_file./2013-05-07T11:38:20Z2013-05-07T11:38:20Z
<p>This would prevent horrors like:</p>
<pre>
$ ../scripts/clonotypeR detect .fastq
[bam_header_read] EOF marker is absent. The input is probably truncated.
[bsw2_aln] fail to open file '.fastq'. Abort!
[samopen] SAM header is present: 169 sequences.
[sam_read1] reference 'SN:TRDV5 LN:344
3
19
3
' is recognized as '*'.
[main_samview] truncated file.
</pre>