Version 1.0.2

• add --test option to run on test data
• enforce samtools version at least 0.1.19

Version 1.0.1

• Bug fix for iva_qc_make_db --add_to_ref
• Installation easier. Now requires pyfastaq version >= 3.10.0, which no longer depends on numpy.

Version 1.0.0

Important bug fix with libraries without overlapping reads, where contig ends were too aggressively trimmed. Defaults now handle both overlapping (ie fragment length <= 2 x read length) and non-overlapping (ie fragment length > 2 x readlength) libraries.

Version 0.11.7

Default value of max_insert changed from 500 to 800.

Bug fixes:

• reads input file could be invalid and IVA would try to assemble anyway
• now dies more gracefully when no contigs made.

Version 0.11.6

Bug fixes:

• stop trying to repeatedly reuse the same seed sequence
• stop writing tiny contig to final output file

Version 0.11.5

Changes to iva_qc:

• modify GAGE code to run on Mac and fixes for some linux versions
• sanity check input contig and embl files and die more gracefully if something wrong

Version 0.11.4

Bug fix when running ratt scripts in iva_qc, now properly fixed from previous release 0.11.3.

Version 0.11.2

Updates to get onto pypi. Now installation should be done with:
pip3 install iva
unless you have a compelling reason to download this tarball insead.

Version 0.11.0

Reduce assembly errors by changing a few default assembly parameters.

Version 0.10.3

Bug fix, iva_qc: catch cases where GAGE fails, but it still reported all the stats we need.