Browse code

update NEWS

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/gmapR@95424 bc3139a8-67e5-0310-9ffc-ced21a209358

Michael Lawrence authored on 13/10/2014 20:08:07
Showing1 changed files
... ...
@@ -1,3 +1,18 @@
1
+CHANGES IN VERSION 1.8.0
2
+-----------------------
3
+
4
+NEW FEATURES
5
+
6
+    o GmapGenomes can be built from any file supported by rtracklayer
7
+      (so 2bit now works, as well as fasta).
8
+
9
+    o Tally BAM files by codon given a set of transcript
10
+      structures. This happens at the read level, i.e., a codon is
11
+      observed within an individual read.
12
+
13
+    o Tally BAM files strand by XS tag (inferred strand of
14
+      transcription, instead of strand of alignment).
15
+    
1 16
 CHANGES IN VERSION 1.6.0
2 17
 -----------------------
3 18
 
Browse code

add NEWS for release

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/gmapR@88834 bc3139a8-67e5-0310-9ffc-ced21a209358

Michael Lawrence authored on 11/04/2014 20:23:34
Showing1 changed files
... ...
@@ -1,3 +1,29 @@
1
+CHANGES IN VERSION 1.6.0
2
+-----------------------
3
+
4
+NEW FEATURES
5
+
6
+    o Add median distance from nearest end (MDFNE) statistics to output
7
+      of variantSummary.
8
+
9
+    o Updated GSNAP, which is orders of magnitude faster than the
10
+      previous version, brings many fixes and offers many new
11
+      features. One new feature is the clip_overlap argument, which
12
+      clips overlapping ends of read pairs (important for variant
13
+      calling).
14
+
15
+    o Updated bam_tally, which is faster and includes support for
16
+      counting in soft-clipped regions.
17
+    
18
+USER-VISIBLE CHANGES
19
+
20
+    o Changes to tallyVariant statistics: drop the unique read
21
+      position counts; renamed count.pos/count.neg to
22
+      count.plus/count.minus (way better names)
23
+
24
+    o tallyVariants does a better job of carrying over the Seqinfo
25
+      from the BAM file.
26
+    
1 27
 CHANGES IN VERSION 1.4.0
2 28
 -----------------------
3 29
 
Browse code

bam_tally annotates columns with Description field for inclusion in VCF header

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/gmapR@82008 bc3139a8-67e5-0310-9ffc-ced21a209358

Michael Lawrence authored on 22/10/2013 22:49:06
Showing1 changed files
... ...
@@ -1,3 +1,44 @@
1
+CHANGES IN VERSION 1.4.0
2
+-----------------------
3
+
4
+NEW FEATURES
5
+
6
+    o Add desired_read_group to BamTallyParam; will limit tallies to
7
+      that specific read group (useful for multi-amplicon sequencing,
8
+      like Fluidigm)
9
+
10
+    o Add keep_ref_rows argument to variantSummary() for keeping rows
11
+      for positions where no alt is detected (the rows where ref == alt).
12
+
13
+    o gsnap() will now output a GsnapOutputList when there are
14
+      multiple input files
15
+
16
+    o Support 'terminal_threshold' and 'gmap_mode' parameters in
17
+      GsnapParam, and use different defaults for DNA vs. RNA. This
18
+      means a big improvement in alignment quality for DNA.
19
+
20
+    o GmapGenome now accepts a direct path to the genome as its first argument
21
+    
22
+USER-VISIBLE CHANGES
23
+
24
+    o Renamed summarizeVariants to variantSummary
25
+
26
+    o The 'which' in GsnapParam is now a GenomicRanges instead of a RangesList
27
+
28
+    o Refactor bam_tally, so that bam_tally returns a TallyIIT object,
29
+      which is then summarized via summarizeVariants; this allows computing
30
+      tallies once and summarizing them in different ways (like maybe get
31
+      the coverage). The summarizeVariants function yields a VRanges.
32
+
33
+BUG FIXES
34
+
35
+    o fix minimum quality cutoff check to >=, instead of >
36
+
37
+    o fix asBam,GsnapOutput for when unique_only is TRUE
38
+
39
+    o package created by makeGmapGenomePackage now have a GmapGenome with
40
+      the correct name
41
+
1 42
 CHANGES IN VERSION 1.2.0
2 43
 -----------------------
3 44
 
Browse code

check in the NEWS file

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/gmapR@75206 bc3139a8-67e5-0310-9ffc-ced21a209358

Michael Lawrence authored on 02/04/2013 22:39:12
Showing1 changed files
1 1
new file mode 100644
... ...
@@ -0,0 +1,30 @@
1
+CHANGES IN VERSION 1.2.0
2
+-----------------------
3
+
4
+NEW FEATURES
5
+
6
+    o New method getSeq,GmapGenome retrieves sequence from a
7
+      GmapGenome index. This also supports a coercion to DNAStringSet
8
+      and thus easy export to FASTA via rtracklayer.
9
+
10
+    o bam_tally gains an ignore_duplicates argument for ignoring BAM
11
+      records flagged as PCR/optical duplicates.
12
+
13
+    o Read position mean and variance are now output by bam_tally.
14
+
15
+USER-VISIBLE CHANGES
16
+
17
+    o GMAP has been updated to the July '12 version (yes, this is old).
18
+    
19
+    o GSTRUCT (bamtally) updated to trunk as of 3/22/13.
20
+    
21
+BUG FIXES
22
+
23
+    o asBam,GsnapOutput now actually works.
24
+
25
+CHANGES IN VERSION 1.0.0
26
+-----------------------
27
+
28
+Initial release
29
+
30
+(start date: 12 September, 2012)