[med-svn] [Git][med-team/tantan][master] 4 commits: New upstream version 50

[Sascha Steinbiss (@satta)]

Sascha Steinbiss pushed to branch master at Debian Med / tantan


Commits:
64a1f177 by Sascha Steinbiss at 2024-08-03T23:54:09+02:00
New upstream version 50
- - - - -
136e6bc7 by Sascha Steinbiss at 2024-08-03T23:54:10+02:00
Update upstream source from tag 'upstream/50'

Update to upstream version '50'
with Debian dir fe24e964eadf1328d5ae32e2ecf4c320e7f3ab8e
- - - - -
02d3d8e6 by Sascha Steinbiss at 2024-08-04T00:00:14+02:00
new upstream version

- - - - -
0e5356d5 by Sascha Steinbiss at 2024-08-04T00:00:32+02:00
bump Standards-Version

- - - - -


7 changed files:

- debian/changelog
- debian/control
- src/Makefile
- src/mcf_fasta_sequence.cc
- + test/semicolons.fa
- test/tantan_test.out
- test/tantan_test.sh


Changes:

=====================================
debian/changelog
=====================================
@@ -1,3 +1,16 @@
+tantan (50-2) unstable; urgency=medium
+
+  * Really bump Standards-Version.
+
+ -- Sascha Steinbiss <satta at debian.org>  Sat, 03 Aug 2024 23:58:14 +0200
+
+tantan (50-1) unstable; urgency=medium
+
+  * New upstream version 50.
+  * Bump Standards-Version.
+
+ -- Sascha Steinbiss <satta at debian.org>  Sat, 03 Aug 2024 23:54:13 +0200
+
 tantan (49-2) unstable; urgency=medium
 
   * Change d/watch to use Git instead of tarballs.


=====================================
debian/control
=====================================
@@ -5,7 +5,7 @@ Section: science
 Priority: optional
 Build-Depends: debhelper-compat (= 13),
                zlib1g-dev
-Standards-Version: 4.6.2
+Standards-Version: 4.7.0
 Vcs-Browser: https://salsa.debian.org/med-team/tantan
 Vcs-Git: https://salsa.debian.org/med-team/tantan.git
 Homepage: https://gitlab.com/mcfrith/tantan


=====================================
src/Makefile
=====================================
@@ -10,7 +10,7 @@ clean:
 	rm -f ../bin/tantan
 
 VERSION1 = git describe --dirty
-VERSION2 = echo ' (HEAD -> main, tag: 49) ' | sed -e 's/.*tag: *//' -e 's/[,) ].*//'
+VERSION2 = echo ' (HEAD -> main, tag: 50) ' | sed -e 's/.*tag: *//' -e 's/[,) ].*//'
 
 VERSION = \"`test -e ../.git && $(VERSION1) || $(VERSION2)`\"
 


=====================================
src/mcf_fasta_sequence.cc
=====================================
@@ -6,6 +6,7 @@
 
 //#include <iostream>  // for debugging
 #include <istream>
+#include <limits>
 #include <ostream>
 #include <streambuf>
 
@@ -19,7 +20,14 @@ static void readSequence(std::istream &s, std::vector<uchar> &sequence,
   while (c != std::streambuf::traits_type::eof()) {
     if (c > ' ') {
       if (c == delimiter) break;
-      sequence.push_back(c);
+      if (c == ';') {  // allow for comment lines starting with ';'
+	do {
+	  c = b->snextc();
+	  if (c == std::streambuf::traits_type::eof()) return;
+	} while (c != '\n');
+      } else {
+	sequence.push_back(c);
+      }
     }
     c = b->snextc();
   }
@@ -40,8 +48,12 @@ static void readQualityCodes(std::istream &s, std::vector<uchar> &qualityCodes,
 }
 
 std::istream &operator>>(std::istream &s, FastaSequence &f) {
-  char firstChar = '>';
-  s >> firstChar;
+  char firstChar;
+  do {
+    firstChar = '>';
+    s >> firstChar;
+  } while (firstChar == ';' &&  // allow for comment lines starting with ';'
+	   s.ignore(std::numeric_limits<std::streamsize>::max(), '\n'));
   if (firstChar != '>' && firstChar != '@') s.setstate(std::ios::failbit);
   if (!s) return s;
 


=====================================
test/semicolons.fa
=====================================
@@ -0,0 +1,14 @@
+; CLUSTER: A12
+; N=4
+>seq1
+ATTTCGCTGATTCGGAT
+>seq2
+ATATCCCTGATTCGGAT
+>seq3
+; del 11:13
+ATATCCCTGACGGATAA
+>seq4
+ACCCCCCTGATTCGGAT
+; CLUSTER: A13 
+>seq5
+AAAAAATCTTTCTTTCT


=====================================
test/tantan_test.out
=====================================
@@ -1535,3 +1535,14 @@ SRR019778.95	2	18	4	4	TGAT	TGAT,TGAT,TGAT,TGAT
 SRR019778.95	22	45	4	5.75	ATAG	ATAG,ATAG,ATAG,ATAG,ATAG,ATA
 
 hard	0	40	5	7.6	ATCAT	CATCAT,CATCAT,CAT-AT,CATAT,CATAT,CATAT,CATAT,CAT
+
+>seq1
+ATTTCGCTGATTCGGAT
+>seq2
+ATATCCCTGATTCGGAT
+>seq3
+ATATCCCTGACGGATAA
+>seq4
+ACCCCCCTGATTCGGAT
+>seq5
+AAAAAATCTTTctttCT


=====================================
test/tantan_test.sh
=====================================
@@ -41,4 +41,6 @@ countLowercaseLetters () {
     tantan -f4 -b0 -j0 panda.fastq
     echo
     tantan -f4 -w7000 hard.fa
+    echo
+    tantan -r0.05 semicolons.fa
 } 2>&1 | diff -u tantan_test.out -



View it on GitLab: https://salsa.debian.org/med-team/tantan/-/compare/fef1d7c20559e28346d3bb53cc805bd29111cc73...0e5356d57dfbcb9e0b9d84ee4e6655a926490c3a

-- 
View it on GitLab: https://salsa.debian.org/med-team/tantan/-/compare/fef1d7c20559e28346d3bb53cc805bd29111cc73...0e5356d57dfbcb9e0b9d84ee4e6655a926490c3a
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