diff --git a/CHANGES b/CHANGES index 9c10f17..4e71a0e 100644 --- a/CHANGES +++ b/CHANGES @@ -1,4 +1,7 @@ Revision history for MinCED +0.1.6 18-Jul-2014 + Fix off-by-one error in the gff output. + 0.1.5 03-Apl-2014 Changed the behaviour of the '-spacers' option. Without any output file given the behaviour is the same as before, creating diff --git a/CRISPR.java b/CRISPR.java index 50dec8e..882cffc 100644 --- a/CRISPR.java +++ b/CRISPR.java @@ -139,7 +139,7 @@ public String toGff(String sequenceName, String parentName) { String str = ""; for (int m = 0; m < numRepeats(); m++) { int repeat_position = (repeatAt(m) + 1); - int repeat_end = repeat_position + this.repeatLength(); + int repeat_end = repeat_position + this.repeatLength() - 1; str += sequenceName + "\tminced:"+minced.VERSION+"\trepeat_unit\t" + repeat_position + "\t" + repeat_end + "\t1\t.\t.\tParent=" + parentName + ";ID=DR"+(m + 1) + "\n"; } return str; diff --git a/CRISPRFinder.java b/CRISPRFinder.java index 9c5fb94..7fe3359 100644 --- a/CRISPRFinder.java +++ b/CRISPRFinder.java @@ -291,7 +291,7 @@ private boolean findRepeats( DNASequence sequence, int readNum ) if(outputformat > 0) { String crispr_id = "CRISPR" + (++totalCrisprCount); out.print(sequence.getName() + "\tminced:" + minced.VERSION + "\tCRISPR\t"); - out.print((currCRISPR.start() + 1) + "\t" + (currCRISPR.end() + 2) + "\t"); + out.print((currCRISPR.start() + 1) + "\t" + (currCRISPR.end() + 1) + "\t"); out.print(currCRISPR.numRepeats() + "\t.\t.\tID="+ crispr_id); out.print("\n"); if(outputformat == 2) { diff --git a/minced.java b/minced.java index f54d0ac..1955844 100644 --- a/minced.java +++ b/minced.java @@ -2,7 +2,7 @@ public class minced { - public static final String VERSION = "0.1.5"; + public static final String VERSION = "0.1.6"; public static void main(String[] args) { //default values