squigulator-v0.5.0

Changes from the previous version are:

• new metadata added to the slow5 data header to make it compatible with newer versions of Dorado basecallers (experiment_name, flow_cell_product_code, protocol_run_id, protocol_start_time, sample_id, sequencer_position, system_name)
• auxiliary field end_reason is now written irrespective of the --ont-friendly=yes option
• experimental --meth-all-ctx=yes/no option. See #29
• minor documentation updates

Full Changelog: v0.4.0...v0.5.0

squigulator-v0.4.0

Changes from the previous version are

• methylation can be now simulated for R9 DNA (--meth-freq option) #8
• option for printing fake UUID readids and end_reason so that software from ONT such as Dorado would be happy (--ont-friendly option) #13
• adding the rna004-min profile for simulating rna004 data for MinION
• minor bug fixes and more test cases added, update slow5lib

squigulator-v0.3.0

Newly added features and major updates in this version compared to previous v0.2.1 are:

• added support for the new RNA004 chemistry
• dna-r10- profiles now generate 5KHz data to match with latest updates to ONT chemistry
• --trans-trunc option for simulating truncated transcript lengths in RNA simulation
• --trans-count option for simulating transcript abundance in RNA simulation
• --cdna option for simulation cDNA data
• two new developer options --median-before-mean and --median-before-std

Documentation newly added:

• parameter profiles: https://hasindu2008.github.io/squigulator/docs/profile.html

Bug fixes:

• --dwell-mean option was mistakenly erroring out which is now fixed

Internal code changes not affecting the user:

• code restructure
• make file updates
• more test cases
• update slow5lib

squigulator-v0.2.2

Changes from v0.2.1 are:

• fix bug where the option for sample rate was not effective
• update readme

squigulator-v0.2.1

Minor bug fix

• c7a1e49: fix a bug that affected the si tag in sam output

squigulator-v0.2.0

New highlights v0.1.0 are:

1. support for R10 data (-x dna-r10-min and dna-r10-prom profiles)
2. ability to output the signal to read/reference annotation in PAF and SAM formats (-a, -c and --paf-ref options, see output description page), that can be visualised with squigualiser
3. More command line fine-tuning parameters (e.g., --amp-noise, --digitisation etc, see man page)
4. New options such as -f for specifying fold coverage and --bps for translocation speed (see man page)

squigulator-v0.1.0

• the very first release