diff -Nru r-bioc-shortread-1.44.1/debian/changelog r-bioc-shortread-1.44.3/debian/changelog
--- r-bioc-shortread-1.44.1/debian/changelog	2019-12-28 21:25:53.000000000 +0000
+++ r-bioc-shortread-1.44.3/debian/changelog	2020-02-07 19:50:24.000000000 +0000
@@ -1,3 +1,11 @@
+r-bioc-shortread (1.44.3-1) unstable; urgency=medium
+
+  * Team upload.
+  * New upstream version
+  * Standards-Version: 4.5.0
+
+ -- Dylan Aïssi <daissi@debian.org>  Fri, 07 Feb 2020 20:50:24 +0100
+
 r-bioc-shortread (1.44.1-1) unstable; urgency=medium
 
   * New upstream version
diff -Nru r-bioc-shortread-1.44.1/debian/control r-bioc-shortread-1.44.3/debian/control
--- r-bioc-shortread-1.44.1/debian/control	2019-12-28 21:25:53.000000000 +0000
+++ r-bioc-shortread-1.44.3/debian/control	2020-02-07 19:50:24.000000000 +0000
@@ -21,7 +21,7 @@
                r-cran-lattice,
                r-cran-latticeextra,
                r-bioc-xvector
-Standards-Version: 4.4.1
+Standards-Version: 4.5.0
 Vcs-Browser: https://salsa.debian.org/r-pkg-team/r-bioc-shortread
 Vcs-Git: https://salsa.debian.org/r-pkg-team/r-bioc-shortread.git
 Homepage: https://bioconductor.org/packages/ShortRead/
diff -Nru r-bioc-shortread-1.44.1/DESCRIPTION r-bioc-shortread-1.44.3/DESCRIPTION
--- r-bioc-shortread-1.44.1/DESCRIPTION	2019-12-20 00:39:14.000000000 +0000
+++ r-bioc-shortread-1.44.3/DESCRIPTION	2020-02-04 00:38:49.000000000 +0000
@@ -1,7 +1,7 @@
 Package: ShortRead
 Type: Package
 Title: FASTQ input and manipulation
-Version: 1.44.1
+Version: 1.44.3
 Author: Martin Morgan, Michael Lawrence, Simon Anders
 Maintainer: Bioconductor Package Maintainer
  <maintainer@bioconductor.org>
@@ -24,8 +24,8 @@
 biocViews: DataImport, Sequencing, QualityControl
 git_url: https://git.bioconductor.org/packages/ShortRead
 git_branch: RELEASE_3_10
-git_last_commit: a5041a8
-git_last_commit_date: 2019-12-19
-Date/Publication: 2019-12-19
+git_last_commit: d97933c
+git_last_commit_date: 2020-02-03
+Date/Publication: 2020-02-03
 NeedsCompilation: yes
-Packaged: 2019-12-20 00:39:14 UTC; biocbuild
+Packaged: 2020-02-04 00:38:49 UTC; biocbuild
Binary files /tmp/tmpGoo1kd/oITx4Jg8zy/r-bioc-shortread-1.44.1/inst/doc/Overview.pdf and /tmp/tmpGoo1kd/NmncpIFpcs/r-bioc-shortread-1.44.3/inst/doc/Overview.pdf differ
diff -Nru r-bioc-shortread-1.44.1/inst/unitTests/test_ShortReadQ.R r-bioc-shortread-1.44.3/inst/unitTests/test_ShortReadQ.R
--- r-bioc-shortread-1.44.1/inst/unitTests/test_ShortReadQ.R	2019-10-29 20:13:34.000000000 +0000
+++ r-bioc-shortread-1.44.3/inst/unitTests/test_ShortReadQ.R	2020-02-03 21:47:07.000000000 +0000
@@ -21,6 +21,17 @@
     checkIdentical(as.character(id(x)), as.character(id(y)))
 }
 
+test_qualityTypeAuto <- function() {
+    .qualityTypeAuto <- ShortRead:::.qualityTypeAuto
+    ## SFastqQuality if all > ':'; some > 'J'
+    quality <- BStringSet(":J")
+    quality <- BStringSet(";J")
+    checkIdentical(.qualityTypeAuto(quality), FastqQuality)
+    checkIdentical(.qualityTypeAuto(quality), FastqQuality)
+    quality <- BStringSet(";K")
+    checkIdentical(.qualityTypeAuto(quality), SFastqQuality)
+}
+
 test_ShortReadQ_constructors <- function() {
     sp <- SolexaPath(system.file('extdata', package='ShortRead'))
     sr <- obj <- readFastq(sp)
diff -Nru r-bioc-shortread-1.44.1/NEWS r-bioc-shortread-1.44.3/NEWS
--- r-bioc-shortread-1.44.1/NEWS	2019-10-29 20:13:34.000000000 +0000
+++ r-bioc-shortread-1.44.3/NEWS	2020-01-31 21:46:44.000000000 +0000
@@ -1,3 +1,12 @@
+CHANGES IN VERSION 1.44
+-----------------------
+
+BUG FIXES
+
+    o (v 1.44.2) readFastq argument qualityType = "Auto" correctly
+      identifies SFastqQuality. See
+      https://github.com/Bioconductor/ShortRead/pull/2
+
 CHANGES IN VERSION 1.37
 -----------------------
 
diff -Nru r-bioc-shortread-1.44.1/R/methods-ShortReadQ.R r-bioc-shortread-1.44.3/R/methods-ShortReadQ.R
--- r-bioc-shortread-1.44.1/R/methods-ShortReadQ.R	2019-10-29 20:13:34.000000000 +0000
+++ r-bioc-shortread-1.44.3/R/methods-ShortReadQ.R	2020-01-31 21:46:44.000000000 +0000
@@ -29,6 +29,18 @@
         id=BStringSet(character(length(sread))))
 })
 
+.qualityTypeAuto <-
+    function(quality)
+{
+    ## all > ':'; some > 'J'
+    breaks <- which(alphabetFrequency(BStringSet(":J"), collapse = TRUE) > 0)
+    alf <- alphabetFrequency(head(quality, 10000), collapse=TRUE)
+    wch <- which(alf != 0)
+    if (any(alf) && (min(wch) > breaks[[1]]) && (max(wch) > breaks[[2]])) {
+        SFastqQuality
+    } else FastqQuality
+}
+
 setMethod(ShortReadQ, c("DNAStringSet", "BStringSet", "BStringSet"),
     function(sread, quality, id, ...,
              qualityType=c("Auto", "FastqQuality", "SFastqQuality"),
@@ -42,15 +54,10 @@
         .throw(SRError("UserArgumentMismatch", conditionMessage(err)))
     })
     tryCatch({
-        qualityFunc <-
-            switch(qualityType, Auto={
-                alf <- alphabetFrequency(head(quality, 10000),
-                                         collapse=TRUE)
-                wch <- which(alf != 0)
-                if (any(alf) && (min(wch) >= 58) && (max(wch) > 74)) {
-                    SFastqQuality
-                } else FastqQuality
-            }, SFastqQuality=SFastqQuality, FastqQuality=FastqQuality)
+        qualityFunc <- switch(qualityType,
+                              Auto = .qualityTypeAuto(quality),
+                              SFastqQuality = SFastqQuality,
+                              FastqQuality = FastqQuality)
         quality <- qualityFunc(quality)
         srq <- 
             if (withIds)