Sascha Steinbiss pushed to branch upstream at Debian Med / tantan
Commits:
64a1f177 by Sascha Steinbiss at 2024-08-03T23:54:09+02:00
New upstream version 50
- - - - -
5 changed files:
- src/Makefile
- src/mcf_fasta_sequence.cc
- + test/semicolons.fa
- test/tantan_test.out
- test/tantan_test.sh
Changes:
=====================================
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/-/commit/64a1f1772d553331bd1058f0591aada6795498d7
--
View it on GitLab:
https://salsa.debian.org/med-team/tantan/-/commit/64a1f1772d553331bd1058f0591aada6795498d7
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