4.3.6

What's Changed

• Update readme by @abhi18av in #223
• Revise NEAT installation instructions in README by @joshfactorial in #234
• Parallelization renaming in the utils folder scripts. by @keshav-gandhi in #244
• Merged template changes and put into new branch for unique PR. by @keshav-gandhi in #243
• Testing CLI and new tests for error and mutation models. by @keshav-gandhi in #245
• One-line change to Options class. by @keshav-gandhi in #247
• Tuple bug fixed. by @keshav-gandhi in #249
• RNG bug found in testing. by @keshav-gandhi in #248
• Splits logic. by @keshav-gandhi in #250
• Adding README changes now that bioconda works. by @keshav-gandhi in #246
• Develop by @joshfactorial in #236

New Contributors

• @abhi18av made their first contribution in #223

Full Changelog: 4.3.5...4.3.6

4.3.5

Numerous bug fixes, tweaks and improvements to NEAT.

What's Changed

• Update ChangeLog with NEAT 4.3.4 and 4.3.3 by @joshfactorial in #182
• Fix vcf creation lag by @joshfactorial in #184
• Fix bam quals by @joshfactorial in #185
• Fix for single-ended reads by @joshfactorial in #186
• 187 incorrect numpy rng endpoint off by one low high by @joshfactorial in #192
• 189 namespace object has no attribute output by @joshfactorial in #195
• Fixing bug in parse_input_vcf call by @joshfactorial in #196
• 198 some minor bugs by @joshfactorial in #199
• 194 softmasking fix by @joshfactorial in #200
• Fix model seq error by @joshfactorial in #201
• Fix fastq qual scores by @joshfactorial in #202
• Fix bam quals by @joshfactorial in #204
• Check slow splits by @joshfactorial in #203
• Coverage looks much less repetetive now by @joshfactorial in #206
• BAM alignments looking better by @joshfactorial in #210
• Check coverage by @joshfactorial in #211
• added a todo by @joshfactorial in #212
• Docs/readme bioconda by @keshav-gandhi in #214
• A variety of testing-related changes. by @keshav-gandhi in #217
• fixing stitch and no fastq by @joshfactorial in #219
• Tables, descriptions, and more. by @keshav-gandhi in #218
• Develop by @joshfactorial in #208

Full Changelog: 4.3.4...4.3.5

4.3.4

Fixed a bug for --no-log flag that was causing it to touch the file anyway. Fixed a bug in produce_bam: false where it was trying to create the intermediate bam unnecessarily, throwing an error.

What's Changed

• Update README.md by @joshfactorial in #180
• Develop by @joshfactorial in #181

Full Changelog: 4.3.3...4.3.4

4.3.2

This release was a refactoring of the parallel code in order to fix some header issues in the final output. We simplified the code, eliminating an extraneous loop that was only running 1 time.

What's Changed

• 172 fix vcf headers by @joshfactorial in #174
• Fixed and cleaned up tests by @joshfactorial in #176
• Develop by @joshfactorial in #175

Full Changelog: 4.3.1...v4.3.2

v4.3.1

What's Changed

• Update ChangeLog.md by @joshfactorial in #157
• Update README.md by @joshfactorial in #158
• Update README.md by @alermol in #159
• Handling missing QUAL in user VCF files by @chenyenchung in #163
• Fix genomic coordinate incorrectly used as array index in quality array update by @chenyenchung in #162
• fixed default output folder name by @joshfactorial in #165
• Feature/integrate parallel into sim by @joshfactorial in #170
• Feature/fix options by @joshfactorial in #171
• Develop by @joshfactorial in #164

New Contributors

• @alermol made their first contribution in #159
• @chenyenchung made their first contribution in #163

Full Changelog: 4.3.0...4.3.1

v4.3.0

Added parallelization to NEAT!

4.2.8

What's Changed

• 130 neat crashes with target bed file 500 lines by @joshfactorial in #131
• Fixes bug with quality score array

Full Changelog: 4.2.7...4.2.8

4.2.7

fixed a bug that was throwing an error when the requested read length was greater than the default.

Full Changelog: 4.2.6...4.2.7

v4.2.6

Bug fixes to the error model creation script (plus a few minor bug fixes discovered along the way).

What's Changed

• Develop by @joshfactorial in #129

Full Changelog: 4.2.5...4.2.6

v4.2.5

Found a couple bugs while doing some refactoring. Adding those to a new spot release, hopefully no one's work has been affected!

What's Changed

• small refactoring for Markov model in development by @joshfactorial in #125

Full Changelog: 4.2.4...4.2.5