ESPRESSO v1.5.0

• Use Smith-Waterman in the C step instead of blastn
• Add --blast option to use blastn as in v1.4.0
• Use annotated gene coordinates to split reads into groups
• Add --alignment_read_groups option to use alignment-based read groups as in v1.4.0
• Refactor ESPRESSO Q to reduce memory usage
• Add script to output corrected SAM files
• Add parasail library and perl module to install script
• Use sort info when checking single-exon reads against isoforms
• Include the sample for each read in intermediate files
• Update estimates of time and memory usage in the README

ESPRESSO v1.4.0

• Update checks that compare alignment and isoform endpoints
  • Add --internal_boundary_limit and --allow_longer_terminal_exons
  • Check shorter ISM chains against longest novel ISM chains
  • Always check individual ISM reads for endpoint compatibility
  • Use the correct endpoint when checking NCD alignments
• Output a summary file from each step
• Add --sort_buffer_size
• Check that input alignments are sorted
• Give an error if unable to use GTF or FASTA input files
• Specify NIC or NNC in compatible isoforms output
• Add Dockerfile
• Improve thread error handling
• Use case-sensitive sort for bedgraph in visualization
• Filter reads missing full sequence in S step

ESPRESSO v1.3.2

• Check if endpoints of an ISM read are compatible with a novel isoform
  • The check was only being applied to annotated isoforms
  • If no isoforms pass the endpoints check then do not assign the read any compatible isoforms
• Set environment variable to ensure standard sorting behavior

ESPRESSO v1.3.1

• Add gene_id to gtf output
• Adjust version checks and allow more recent nhmmer versions
• Handle 'X' and '=' cigar operations
• Fix bug when Q step is run with minimal arguments
• Handle secondary alignments
• Update how reads are split for C steps
• Improve error message when chr from alignment is not found in reference fasta
• Fix bug where start of novel isoform was off by 1 in gtf output
• Add automated tests
• Improve thread error checking
• Add sorting to get deterministic novel isoform IDs

ESPRESSO v1.3.0-beta

• Add scripts to split reads for ESPRESSO_C jobs
• Improve how read and SJ inputs are given to blast
• Add threads to ESPRESSO_Q
• Create a pool of worker threads at the beginning of ESPRESSO_S
• Only check certain single exon isoforms for each group
• Ensure consistent output by sorting
• Add version information to gtf output

ESPRESSO v1.2.2

Initial commit: ESPRESSO alpha1.2.2