Steffen Möller pushed to branch master at Debian Med / rna-star
Commits: ced0e9fb by Steffen Moeller at 2018-10-23T11:28:21Z New upstream version 2.6.1c+dfsg - - - - - 8cb1fe86 by Steffen Moeller at 2018-10-23T11:28:22Z Update upstream source from tag 'upstream/2.6.1c+dfsg' Update to upstream version '2.6.1c+dfsg' with Debian dir 3b8d560389d521ad76eba1fee17ecff271c06bae - - - - - 264871e9 by Steffen Moeller at 2018-10-23T11:29:40Z Prepare for new upstream version. - - - - - 830c815a by Steffen Moeller at 2018-10-23T11:31:56Z New upstream version 2.6.1c+dfsg - - - - - 6c0fc528 by Steffen Moeller at 2018-10-23T11:31:57Z Update upstream source from tag 'upstream/2.6.1c+dfsg' Update to upstream version '2.6.1c+dfsg' with Debian dir 4ed65df0d4142e45dd1cbdadfe182f6bb03e235a - - - - - 6 changed files: - CHANGES.md - debian/changelog - source/ReadAlign_chimericDetectionPEmerged.cpp - source/SequenceFuns.cpp - source/VERSION - source/readLoad.cpp Changes: ===================================== CHANGES.md ===================================== @@ -1,3 +1,8 @@ +STAR 2.6.1c 2018/10/17 +====================== + +* Enforced the consistent choice of supplementary chimeric alignments for overlapping mates. + STAR 2.6.1b 2018/09/06 ====================== ===================================== debian/changelog ===================================== @@ -1,3 +1,9 @@ +rna-star (2.6.1c+dfsg-1) unstable; urgency=medium + + * New upstream version. + + -- Steffen Moeller <[email protected]> Tue, 23 Oct 2018 13:28:51 +0200 + rna-star (2.6.1b+dfsg-1) unstable; urgency=medium * New upstream version. ===================================== source/ReadAlign_chimericDetectionPEmerged.cpp ===================================== @@ -39,7 +39,7 @@ void ReadAlign::chimericDetectionPEmerged(ReadAlign &seRA) { }; }; for (uint jj=0; jj<2; jj++) { - if (segLen[ii][jj]<segLmin) { + if (segLen[ii][jj]<segLmin || (segLen[ii][jj]==segLmin && trChim[ii].exons[0][EX_G]>trChim[ii-1].exons[0][EX_G])) { segLmin=segLen[ii][jj]; i1=ii;//trChim of the shortest segment length i2=jj;//mate of the shortest segment length ===================================== source/SequenceFuns.cpp ===================================== @@ -139,7 +139,7 @@ void convertNucleotidesToNumbers(const char* R0, char* R1, const uint Lread) {// case (84): case(116): R1[jj]=char(3);break;//T default: - R1[jj]=char(9);//anything else + R1[jj]=char(4);//anything else is converted to N }; }; }; @@ -160,7 +160,7 @@ uint convertNucleotidesToNumbersRemoveControls(const char* R0, char* R1, const u if (int(R0[jj]) < 32) {//control characters are skipped continue; } else {//all non-control non-ACGT characters are convreted to N - R1[jj]=char(9);//anything else + R1[jj]=char(4);//anything else }; }; ++iR1; ===================================== source/VERSION ===================================== @@ -1 +1 @@ -#define STAR_VERSION "STAR_2.6.1b" +#define STAR_VERSION "STAR_2.6.1c" ===================================== source/readLoad.cpp ===================================== @@ -84,7 +84,7 @@ int readLoad(istream& readInStream, Parameters& P, uint iMate, uint& Lread, uint } else { Lread=0; }; - convertNucleotidesToNumbers(Seq+P.clip5pNbases[iMate],SeqNum,Lread); + convertNucleotidesToNumbersRemoveControls(Seq+P.clip5pNbases[iMate],SeqNum,Lread); //clip the adapter if (P.clip3pAdapterSeq.at(iMate).length()>0) { View it on GitLab: https://salsa.debian.org/med-team/rna-star/compare/088d0682ff48578120a2295297796e4312daf4e1...6c0fc528f72f6a6842d90ba18fd9875c002900fc -- View it on GitLab: https://salsa.debian.org/med-team/rna-star/compare/088d0682ff48578120a2295297796e4312daf4e1...6c0fc528f72f6a6842d90ba18fd9875c002900fc You're receiving this email because of your account on salsa.debian.org.
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