SEM v1.3.0

Use SAMFilePEHitLoader as default hitloader, resolve the issue that exact second read 5' end pos is hard to deduct from the first read

Now SEM is able to process sorted (either name or coordinate sorted) pair-end bam file without the need of filtering reads by flags

Packed based on seqcode-core commit @9f2682a4125ec08d690cf9ca123fd966bc38df1a

SEM v1.2.3

Increase default EM window size to 50000 to reduce the effect of splitter nucleosome at EM window boundary

Note: this is the version used in the manuscript

Full Changelog: v1.2.2...v1.2.3

SEM v1.2.2

Fix the mistake in log likelihood computation step

Full Changelog: v1.2.1...v1.2.2

SEM v1.2.1

add new option --bmanalysiswindowmax for adjusting preferred potential region length

Full Changelog: v1.2.0...v1.2.1

SEM v1.2.0

New figure output and some optimization

• Now SEM would plot a line chart on the fragment size distribution of each nucleosome type
• "--onlyGMM" option for users to run only GMM without nucleosome calling, for optimizing GMM related parameters

Full Changelog: v1.1.2...v1.2.0

SEM v1.1.2

Improvement and bug fixed:

1. Now '--help' parameter can print help message
2. User-provided regions would be first truncated to remove chromosome prefixes to be compatible with the Genome object

Full Changelog: v1.1.1...v1.1.2

SEM v1.1.0

New features:

1. User can provide customized binding subtypes by
   --providedBindingSubtypes
2. User can provide customized potential regions by
   --providedPotentialRegions
3. Cleaner help message

Full Changelog: https://github.com/YenLab/SEM/commits/v1.1.0

SEM v1.0.0

SEM for manuscript

Full Changelog: https://github.com/YenLab/SEM/commits/v1.0.0