[med-svn] [Git][med-team/stacks][master] 5 commits: New upstream version 2.54+dfsg
Steffen Möller
gitlab at salsa.debian.org
Tue Sep 15 02:25:15 BST 2020
Steffen Möller pushed to branch master at Debian Med / stacks
Commits:
1cf01362 by Steffen Moeller at 2020-09-15T03:15:53+02:00
New upstream version 2.54+dfsg
- - - - -
d9771e76 by Steffen Moeller at 2020-09-15T03:15:53+02:00
routine-update: New upstream version
- - - - -
45e0caed by Steffen Moeller at 2020-09-15T03:15:54+02:00
Update upstream source from tag 'upstream/2.54+dfsg'
Update to upstream version '2.54+dfsg'
with Debian dir b1e68f504dd442a47c3000b0110464a61bd7a65a
- - - - -
58da5d51 by Steffen Moeller at 2020-09-15T03:15:54+02:00
routine-update: debhelper-compat 13
- - - - -
0b3b8c43 by Steffen Moeller at 2020-09-15T03:23:59+02:00
routine-update: Ready to upload to unstable
- - - - -
7 changed files:
- ChangeLog
- configure.ac
- debian/NEWS.Debian → debian/NEWS
- debian/changelog
- debian/control
- scripts/stacks-integrate-alignments
- src/renz.cc
Changes:
=====================================
ChangeLog
=====================================
@@ -1,3 +1,8 @@
+Stacks 2.54 - September 03, 2020
+--------------------------------
+ Feature: Added BtgI, PacI, and PspXI, HpyCH4IV restriction enzymes to process_radtags.
+ Bugfix: stacks-integrate-alignments, tab characters fed to the grep were not being interpreted properly
+
Stacks 2.53 - March 28, 2020
----------------------------
Bugfix: denovo_map.pl was broken for running cstacks on non-genetic map datasets.
=====================================
configure.ac
=====================================
@@ -2,7 +2,7 @@
# Process this file with autoconf to produce a configure script.
AC_PREREQ(2.59)
-AC_INIT([Stacks], [2.53])
+AC_INIT([Stacks], [2.54])
AC_CONFIG_AUX_DIR([config])
AM_INIT_AUTOMAKE([-Wall -Werror foreign parallel-tests subdir-objects])
AC_CONFIG_SRCDIR([src/ustacks.cc])
=====================================
debian/NEWS.Debian → debian/NEWS
=====================================
=====================================
debian/changelog
=====================================
@@ -1,3 +1,12 @@
+stacks (2.54+dfsg-1) unstable; urgency=medium
+
+ * Team upload.
+ * New upstream version
+ * debhelper-compat 13 (routine-update)
+ * Lintian warned: d/NEWS.Debian -> d/NEWS
+
+ -- Steffen Moeller <moeller at debian.org> Tue, 15 Sep 2020 03:16:02 +0200
+
stacks (2.53+dfsg-1) unstable; urgency=medium
* Team upload.
=====================================
debian/control
=====================================
@@ -4,7 +4,7 @@ Uploaders: Tim Booth <tbooth at ceh.ac.uk>,
Andreas Tille <tille at debian.org>
Section: science
Priority: optional
-Build-Depends: debhelper-compat (= 12),
+Build-Depends: debhelper-compat (= 13),
zlib1g-dev,
libbam-dev,
libsparsehash-dev,
=====================================
scripts/stacks-integrate-alignments
=====================================
@@ -116,7 +116,7 @@ samtools view -F 0x904 "$bam_f" |
join -t $'\t' -12 -22 -o "1.1 1.2 2.1 1.3 1.4" \
- \
<(samtools view -H "$bam_f" |
- grep '^@SQ' | grep -oE 'SN:[^\t]+' | cut -c4- |
+ grep '^@SQ' | grep -oE $'SN:[^\t]+' | cut -c4- |
awk '{printf NR"\t"$1"\n"}' |
sort -k2,2
) |
=====================================
src/renz.cc
=====================================
@@ -36,6 +36,8 @@ const char *bspDI[] = {"CGAT", // AT/CGAT, BspDI
"ATCG"};
const char *bstYI[] = {"GATCC", "GATCT", // R/GATCY, BstYI (also known as PsuI)
"GGATC", "AGATC"};
+const char *btgI[] = {"CACGG", "CGCGG", "CATGG", "CGTGG", // C/CRYGG, BtgI
+ "CCGTG", "CCGCG", "CCATG", "CCACG"};
const char *cac8I[] = {"AGC", "CGC", "GGC", "TGC", // GCN/NGC, Cac8I
"GCT", "GCG", "GCC", "GCA"};
const char *claI[] = {"CGAT", // AT/CGAT, ClaI
@@ -62,6 +64,8 @@ const char *hindIII[] = {"AGCTT", // A/AGCTT, HindIII
"TCGAA"};
const char *hpaII[] = {"CGG", // C/CGG, HpaII
"CCG"};
+const char *hpyCH4IV[] = {"CGT", // A/CGT, HpyCH4IV
+ "ACG"};
const char *kpnI[] = {"GTACC", // C/CATGG, KpnI
"GGTAC"};
const char *mluCI[] = {"AATT", // AATT, MluCI
@@ -98,6 +102,10 @@ const char *nsiI[] = {"TGCAT", // ATGCA/T, NsiI
"ATGCA"};
const char *nspI[] = {"CATGA", "CATGG", // R/CATGY, NspI
"GCATG", "ACATG"};
+const char *pacI[] = {"ATTAA", // AAT/TAATT, PacI
+ "TTAAT"};
+const char *pspXI[] = {"TCGAGC", "TCGAGG", "TCGAGT", // VC/TCGAGB, PspXI
+ "GCTCGA", "CCTCGA", "ACTCGA"};
const char *pstI[] = {"TGCAG", // CTGCA/G, PstI
"CTGCA"};
const char *rsaI[] = {"AC", // GT/AC, RsaI
@@ -178,6 +186,10 @@ initialize_renz(map<string, const char **> &renz, map<string, int> &renz_cnt, ma
renz["apaLI"] = apaLI; // G/TGCAC, ApaLI
renz["hinP1I"] = hinP1I; // G/CGC, HinP1I
renz["bbvCI"] = bbvCI;
+ renz["btgI"] = btgI; // C/CRYGG, BtgI
+ renz["pacI"] = pacI; // AAT/TAATT, PacI
+ renz["pspXI"] = pspXI; // VC/TCGAGB, PspXI
+ renz["hpyCH4IV"] = hpyCH4IV; // A/CGT, HpyCH4IV
renz_cnt["sbfI"] = 1;
renz_cnt["pstI"] = 1;
@@ -231,7 +243,11 @@ initialize_renz(map<string, const char **> &renz, map<string, int> &renz_cnt, ma
renz_cnt["apaLI"] = 1;
renz_cnt["hinP1I"] = 1;
renz_cnt["bbvCI"] = 1;
-
+ renz_cnt["btgI"] = 4;
+ renz_cnt["pacI"] = 1;
+ renz_cnt["pspXI"] = 3;
+ renz_cnt["hpyCH4IV"] = 1;
+
renz_len["sbfI"] = 6;
renz_len["pstI"] = 5;
renz_len["notI"] = 6;
@@ -284,6 +300,10 @@ initialize_renz(map<string, const char **> &renz, map<string, int> &renz_cnt, ma
renz_len["apaLI"] = 5;
renz_len["hinP1I"] = 3;
renz_len["bbvCI"] = 5;
+ renz_len["btgI"] = 5;
+ renz_len["pacI"] = 5;
+ renz_len["pspXI"] = 6;
+ renz_len["hpyCH4IV"] = 3;
}
void
View it on GitLab: https://salsa.debian.org/med-team/stacks/-/compare/7df2bfc5e945406aceb414a3c25b928aea76c2ed...0b3b8c437f0764ab75a884519ebcfc7019feebab
--
View it on GitLab: https://salsa.debian.org/med-team/stacks/-/compare/7df2bfc5e945406aceb414a3c25b928aea76c2ed...0b3b8c437f0764ab75a884519ebcfc7019feebab
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