Strawberry v1.1.2

Update README.md

Strawberry v1.1.1

1. Remove unnecessary assertion.
2. Fix segfalut.

Strawberry v1.1.0

1. Adding ref_gene_id and ref_gene_name fields to output gtf file, if reference guided assembly is used. These are taken from the matched reference loci.
2. When running with --no-quant flag, TPM and FPKM parts from the output gtf file will be omitted.
3. The --output-dir option is changed to --output-gtf option.
4. The logfile now by default is saved to /tmp/strawberry.log
5. Fix mem bugs. Some details see: #33 and #36.

Strawberry 1.0.5

1. Update -g option. When using reference annotations, the closest gene id/symbol will be added to the output gtf file.
2. Bug fix for loading transcripts.

Strawberry-long-1.0.2

Fix a bug when loading the last transcript is out of bound.

Strawberry-long-1.01

1. Add Pacbio ccs read support.
2. Update logging.

0.9.3

1. Fix issue #20. This bug is trigger by using gencode.v28.annotation.gtf, which contains a 1 bp intron. Thanks for @47Lies for reporting this bug and providing the test case!

2. Fix a bug when a bam file contains number only contig/scaffold names. This bug caused dropping all reads.

0.9.2 Add Strand specific options

Add Strand-specific options:
--fr assumes stranded library fr-secondstrand
--rf assumes stranded library rf-firststrand
If none of them is specified the default is the non-strand specific library.