Changes

0.01  Tue Jun 18 19:11:02 2013
	- original version; created by h2xs 1.23 with options
		-AXc -n BedAnno -b v5.10.1

0.10  Mon Jul 08 17:01:02 2013
	- alpha version released.

0.11  Mon Jul 08 22:01:02 2013
	- add method write_using() to generate db information files.

0.12  Tue Jul 09 13:01:02 2013
	- fix a bug in parse_cPos, when dealing with intron mutation

0.13  Tue Jul 09 22:32:02 2013
	- add a new type 'c' to write_using() method to make the
	  complete annotation region be available to generate.

0.14  Wes Jul 10 13.14:02 2013
	- fix a bug of typo in parse_var()

0.15  Sun Jul 14 22:04:01 2013
	- support character 'N' in the variation string
	- add a exported method individual_anno() to combinate 
	  two variation in one individual.

0.16  Sun Jul 16 16:17:01 2013
	- fix bugs in write_using()
	- add a method get_cover_batch() to fetch cPos information 
	  of region in batch mode
	- add comments for annodb format.

0.17  Thu Jul 18 19:58:02 2013
	- add an exported method get_gHGVS which generate 'g./m.' HGVS string

0.18  Tue Jul 23 20:30:01 2013
	- fix a few bugs
	- add more test cases

0.19  Thu Jul 25 15:00:00 2013
	- change the library to not to use perl v5.10 feature, change all 
	  given/when structure to if/elsif structure. for furture compatible
	  issues.

0.20  Thu Jul 26 21:03:03 2013
	- fix a bug in get_internal()
	- add various test cases

0.30  Thu Aug 21 11:43:07 2013
	- change the structure of return value for pairanno(), 
	  move the strd information out of the flanks infomations 
	  as an outer key.
	- change function of 'altstart' to 'misstart'

0.31  Thu Aug 24 09:06:08 2013
	- change to support short peptide code annotation by add a new 
	  parameter: "short", in the 'new' method. e.g.

0.32  Tue Oct 08 16:43:01 2013
	- change internal tech and db format to support CG's shell list and VCF,
	  also will change to annotate on real refSeq sequence, not the cut 
	  from refgenome pseudo ones.

0.33  Tue Oct 22 17:26:30 2013
	- fix some bugs and release a new revision version for future test-cases.

0.34  Mon Oct 28 22:38:06 2013
	- add a method decide_major for crawler to generate 
	  TranscriptVarName from major transcript
	- The reformatAnno() will have a new key "TranscriptVarName" in 
	  "var" to give the value please use "man doc/BedAnno.1" to 
	  check the detail in "decide_major" method description

0.35  Sat Nov 02 18:43:05 2013
	- change to use Tabix Perl API instead of system call cmd: tabix

0.36  Wed Nov 06 14:44:04 2013
	- get rid of fetchseq by samtools faidx, hash all transcript 
	  sequences at the very beginning.

0.37  Fri Nov 15 20:13:43 2013
	- fix bugs for many different special variants position or sequence states

0.38  Tue Nov 20 00:18:01 2013
	- fix a bug for edge insertion case

0.39  Wed Dec 04 19:39:05 2013
	- fix some minor bugs
	- add trWalker method to uniform the cHGVS string to give 
	  3-END most variation and recognize whole repeat region 
	  case in transcripts.

0.40  Wed Dec 11 22:30:06 2013
	- add condel score and prediction, based on the 
	  VEP_plugins/Condel.pm version 2.4
	  The scores seem a little different from the VEP version 2.6's result, 
	  though the prediction are the same from checking one of example var.
	- add an option 'quiet' to suppress warning information for 
	  extra database query.
	- change master branch to not to use threads::shared
	- add repeat tag extradb and api.
	- allow remaining extra information in the BedAnno::Var entry 
	  by using hash ref input.
	- fix BedAnno::Var->new for VCF reference variant parsing.
	- reformatAnno() is changed to give uniform begin/end position

0.41  Wed Feb 19 14:44:44 2014
	- for crawler need, move TranscriptVarName to VarName
	- for crawler need, move GenePartIndex to ComponentIndex
	- for crawler need, add ImpactIndex, GenePartIndex, varTypeIndex
	- for crawler need, add trVarName for each transcript.
	- add varName to var hash, add trVarName to trInfo tr hash.

0.42  Mon Mar 03 15:15:15 2014
	- add DESTROY method to prevent memory leak.

0.43  Wes Mar 05 13:45:45 2014
	- fix bugs for cds exon-intron edge insertion variants.

0.44  Thu Mar 06 13:58:58 2014
	- fix a bug for using trans options to limit annotation.

0.45  Thu Mar 13 11:18:23 2014
	- fix a problem when repeat get across two different region,
	  original cHGVS will give the repeat format cHGVS, and for now,
	  it will give it as a delins.
	- add new keys alt_cHGVS and alt_pHGVS to transcript var hash
          to give a backward compatible HGVS naming for repeat format
	  HGVS, which can be easily used to query public databases.

0.46  Mon Mar 17 12:20:12 2014
	- fix a bug for middle intron variant
	- fix exon region no-call notation, change '=' to actual base
	- fix p.= to p.(=)

0.47  Tue Mar 18 09:49:50
	- fix cDot name for del and delins case, with adding the deleted bases.
	- fix a bug in exon-intron span case
	- add a limitation of repeat parsing, for time consuming.
	- fix a minor problem for outside promoter region span case
	- fix a 'fs*1' problem

0.48  Mon Mar 24 19:33:20
	- fix reformatAnno to give chromosome a "chr" prefix.
	- fix protBegin for frameshift variant with skipping the same bases.

0.49  Tue Mar 25 22:04:00
	- enhance pDot name to add prWalker to allow protein variant walk around
	  It'll allow tandom protein seq repeat to be called following the 3'most 
	  rule, and only will be difference to previous notation when there 
	  exists a tandom repeat protein sequence which its nucleotide 
	  sequence is not tandom repeat.

0.50  Wed Mar 26 19:55:00
	- uniform HGVS notation by add standard_xHGVS for repeats, 
	  original alt_xHGVS has changed to del/ins format notation

0.51  Thu Mar 27 13:46:23
	- fix a bug for standard_pHGVS and add 3 letter format pHGVS in hash

0.52  Tue Apr 01 15:45:12
	- uniform the prediction words for AE

0.53  Wed Apr 02 16:21:30
	- change translation seq - protein seq length differ 
	  transcript to be annotation-fail

0.54  Thu Apr 03 19:41:20
	- add get_cover_batch to generate region information for given regions

0.55  Fri Apr 04 13:00:05
	- change get_cover_batch to backward compatible to BedAnno v0.32

0.56  Fri Apr 18 10:02:01
	- fix a problem for some special codon '?'
	- fix function code of fs*1 frameshift to nonsense

0.57  Wed Apr 23 20:05:12
	- add support custom frequency db
	  multiple dbs will require similar multiple options

0.58  Mon Apr 28 09:20:12
	- remove unavailable resource

0.59  Fri May 09 16:14:23
	- add alternative pHGVS string for synonymous variant.

0.60  Thr Jul 10 09:42:21
	- fix a bug in getTrChange for 3U span case
	- fix a problem for batched process when multiple same start 
	  blocks hit one same edge position

0.61  Tue Jul 15 17:53:30
	- fix a problem for insertion of stop codon.

0.62  Wed Jul 16 09:12:31
	- fix a problem for N-called no call variant.
	- fix a bug for trWalker and prWalker for walking to the ends.

0.70  Tue Jul 22 17:28:21
	- add BedAnno::CNV child module to annotate CNV in batch mode.

0.71  Wed Jul 23 11:38:22
	- add single cnv var anno method annoCNV()

0.72  Sat Sep 27 13:49:13
	- fix bug in BedAnno for mismatch block edge insertion variant
	- fix problem for primary tag assignment when using LRG_refGene, 
	  without reference standard transcript. (db changed)
	- fix problem for 3bp ranged neighbor ins/del/delins mismatch 
	  caused curious annotation by merging to large delins. (db changed)
	- fix to support annotation for transcript with originally 
	  containing frameshift-site. (db and module changed)

0.73  Tue Oct 21 10:42:23
	- add support to annotate edge span case transcript (db and module changed)

0.74  Wed Oct 22 10:03:45
	- change genepart of splice/intron span case to splice site genepart
	- change edge insertion case genepart to span
	- change to show componentIndex of promoter-5'utr, 3'utr-3'downstream span case.
	- assign the 5' start position's componentIndex as the one of span case

0.75  Fri Oct 24 09:41:22
	- change to give affected protein coordinates for all kinds of variants
        - change to support auto checking canonical splice site for substitution 
          in splice region

0.76  Mon Oct 27 15:14:23
	- fix a bug in intron genepart assignment

0.77  Fri Nov 07 16:13:35
	- change to add support to 4 alternative splice related function recognise.
	  with adding 3 new keys: alt_func alt_funcSO and alt_funcSOname to trInfo's subhash.
	  The priority of these 4 function code is 
	    "exon-loss | splice-5-5th > splice-region > splice-ext"
	  They can not be shown at the same time, becase their definition are overlapped with
          each other.

0.78  Tue Nov 18 10:35:12
	- correct mitochondrial genes symbol to its original format
	- add support to query ExAC database, depend on new plugin: GetExAC.pm

0.79  Wed Nov 19 16:28:21
	- change reformatAnno to group allele frequency together.

0.80  Wed Dec 02 16:34:04
	- change cnv annotation to support sfari database.

0.81  Mon Dec 15 13:17:05
	- fix a problem for 3'downstream var next to bad alignment block.

0.82  Wed Dec 25 11:17:08
	- fix to change indel caused stop_gained to frameshift

0.83  Mon Jan 12 16:40:01
	- fix a bug for ins badaln annotation.

0.84  Tue Jan 13 16:03:01
	- add DistanceToExon for crawler.

0.85  Wed Jan 14 18:00:00
	- add cnvd for cnv anno

0.86  Fri Feb 27 16:16:01
	- fix long reference case to give annotation anyway.

0.88  Wed Apr 29 15:00:01
    - remove reformat_anno method from BedAnno

1.00  Sat May 7 18:00:01
    - update to HGVS version 2.1511

1.01  Thu Mar 17 00:10:00
    - correct a probleam of mutation with stop codon inserted in, the pHGVS is corrected now.

1.11  Fri Apr 7 08:54:12
    - Add gnomAD query API and corresponding info hash

1.12  Thu Aug 17 18:06:12
    - Change to use TGP's new API, not only frequency information, but also other infomation is involved in hash

1.13  Fri Sep  8 13:41:49
    - Change fs1 frameshift to show fs*1 in pHGVS to be used to differ from nonsense mutation

1.15  Wes Nov 21 18:24:31
    - Change population database quering when variant alleles are pseudo mnv.

1.16  Wes Apr 3  19:04:23
    - Change to let db query without repeat format

1.17  Wes May 29 15:35:14
    - fix a bug for inframe insertion just before stop codon

1.18  Wes Jul 03 14:12:21
    - fix a bug for snv around DI mismatch anno problem

1.19  Thr Aug 15 09:05:11
    - fix a bug for annotating stop-loss mutation to frameshift

1.20  Tue Nov 5 13:47:11
    - Due to IO::Compression update, change parameter to fit the update changes.

1.21  Thr Nov 12 20:38:14
    - Change getUnifiedVar to give absolutely left or right aligned result without consider the repeat elements when "norep" is set to 1.
    - fix a minor problem when occasionally the common part of ref and alt allele contains concordant repeats which is not the repeat variants unit.

1.22  Mon Dec  7 11:48:37 2020
    - add standard_cHGVS key for delXXXinsXXX format cHGVS annotation.

1.23  Tue Apr  6 17:52:33 2021 
    - add standard_cHGVS for gene flanking region cHGVS annotation.

1.24  Thu Jul  8 13:29:19 2021
    - fix a bug for using csto as the cds length error in stoploss snv mutation annotation, which leads the error extent length.

1.25  Wed 07 Sep 2022 12:09:17 PM CST
    - fix a bug referenced in issue 15 which influence the multiple aa synonymous variants pDot annotation.

2.00  Fri 16 Sep 2022 09:30:59 AM CST
    - change to multiple mudole structure