If you've found a bug in clonotypeR, post about it here. TODO items go elsewhere. Link items to done when done.

The shortcut commit points to http://source.clonotyper.branchable.com/?p=source.git;a=commitdiff;h=%s. You can use it to link to the commit that fixed the bug, as in [[!commit 7cf11805d84ff8dc6a537c17e73efa275077915d]].

There are 3 "open" bugs:

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clonotypeR detect should test the existence of the FASTQ file.

This would prevent horrors like:

$ ../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



' is recognized as '*'.
[main_samview] truncated file.