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Commits on Sep 4, 2018

• basic XS inference for ref-overlapping alns

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Commits on Aug 29, 2018

• set default -M back to 1.0; version bumped to 1.3.5

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Commits on Jul 19, 2018

• added clipL, clipR soft-clipping values to GBamRecord

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Commits on Jul 13, 2018

• more MacOS gdb fixes

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Commits on Feb 20, 2018

• adjusted Makefile; more -v logging info per bundle

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Commits on Feb 15, 2018

• new version tag due to horrible GStr bug

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Commits on Feb 2, 2018

• bump version to 1.3.4beta due to more GFF parsing changes

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• a few more minor performance tweaks

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• more GTF/GFF parsing fixes and workarounds

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Commits on Dec 14, 2017

• removed unused function

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• a couple of comments added about the consumer-producer model employed

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Commits on Oct 26, 2017

• more stringent recognition of transcripts (only exon-based entities are loaded)

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Commits on Mar 27, 2017

• patch release v1.3.3b

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Commits on Feb 15, 2017

• v1.3.3: fixed TPM and coverage calculation for -G

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Commits on Jan 29, 2017

• v1.3.1d: fixed too permissive GFF parsing bug in gclib

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Commits on Jan 27, 2017

• fixed dumb crash in GTF parsing

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Commits on Jan 24, 2017

• fixed ordering comparator bug which caused a crash in some situations

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Commits on Jan 18, 2017

• turn off GFF debug

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Commits on Jan 17, 2017

• WIP: adjust GTF parsing

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Commits on Dec 23, 2016

• added stranded library options; fixed one base exon crash; fixed duplicate printing of transcripts

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Commits on Nov 22, 2016

• re-fix of samtools aux tag parsing bug using htslib code

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Commits on Nov 16, 2016

• finally found the GBitVec error cause, fixed

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Commits on Nov 15, 2016

• bug fix for an index out of range error in v1.3.1

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Commits on Nov 12, 2016

• final v1.3.1

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  33aa13f

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• v1.3.1 fixes:

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Commits on Nov 1, 2016

• actual fix for old Gencode GTF

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Commits on Sep 7, 2016

• v1.3.0 with improved abundance estimation algorithm; UCSC GTF parsing fix

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Commits on May 12, 2016

• added --bam option for stdin streaming; now skipping invalid mappings (mapped_len<10 or pos<1)

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Commits on May 11, 2016

• hashread improved using a fixed prefix

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• adding per-thread stack size control

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• fixed a few typos

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  b66a21d

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• removed _POSIX_SOURCE #define which can cause problems on OS X

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• retained intron option, collapse of reads for merge option

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• let GffReader close the guides file

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• v1.2.2 fixes, bundling guides that may overlap another guide before the first read in the bundle

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