broadinstitute / viral-ngs / 2349

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travis-ci

trinity hardening (#347)

* better error handling when Trinity fails to assemble.

* more defending against empty inputs along the assembly chain

* fixes to fastq counting and test function names

* moved count_fastq_reads() to util/file.py; refactored to use grep counting on non-gzip files

moved count_fastq_reads() to util/file.py; refactored to use grep
counting on non-gzip files which seems to be faster on Pythons <3.5.
changed fasta_length() to use grep_count() which is also used by
count_fastq_reads()

68 of 68 new or added lines in 2 files covered. (100.0%)

5125 of 7233 relevant lines covered (70.86%)

2.11 hits per line