diff --git a/src/main/java/org/broad/igv/batch/CommandExecutor.java b/src/main/java/org/broad/igv/batch/CommandExecutor.java index e650157343..d26253185f 100755 --- a/src/main/java/org/broad/igv/batch/CommandExecutor.java +++ b/src/main/java/org/broad/igv/batch/CommandExecutor.java @@ -921,6 +921,8 @@ private static AlignmentTrack.SortOption getAlignmentSortOption(String str) { return AlignmentTrack.SortOption.MATE_CHR; } else if (str.equalsIgnoreCase("readOrder")) { return AlignmentTrack.SortOption.READ_ORDER; + } else if (str.equalsIgnoreCase("readname")) { + return AlignmentTrack.SortOption.READ_NAME; } else { try { return AlignmentTrack.SortOption.valueOf(str.toUpperCase()); diff --git a/src/main/java/org/broad/igv/sam/AlignmentTrack.java b/src/main/java/org/broad/igv/sam/AlignmentTrack.java index 5b985f30ff..f4a902666a 100644 --- a/src/main/java/org/broad/igv/sam/AlignmentTrack.java +++ b/src/main/java/org/broad/igv/sam/AlignmentTrack.java @@ -96,7 +96,7 @@ enum ColorOption { public enum SortOption { START, STRAND, NUCLEOTIDE, QUALITY, SAMPLE, READ_GROUP, INSERT_SIZE, FIRST_OF_PAIR_STRAND, MATE_CHR, TAG, - SUPPLEMENTARY, NONE, HAPLOTYPE, READ_ORDER + SUPPLEMENTARY, NONE, HAPLOTYPE, READ_ORDER, READ_NAME } public enum GroupOption { @@ -1633,6 +1633,7 @@ void addSortMenuItem() { mappings.put("sample", SortOption.SAMPLE); mappings.put("read group", SortOption.READ_GROUP); mappings.put("read order", SortOption.READ_ORDER); + mappings.put("read name", SortOption.READ_NAME); if (dataManager.isPairedEnd()) { mappings.put("insert size", SortOption.INSERT_SIZE); diff --git a/src/main/java/org/broad/igv/sam/Row.java b/src/main/java/org/broad/igv/sam/Row.java index a3adf64021..c027041bc6 100644 --- a/src/main/java/org/broad/igv/sam/Row.java +++ b/src/main/java/org/broad/igv/sam/Row.java @@ -97,7 +97,6 @@ public double calculateScore(AlignmentTrack.SortOption option, double center, Al else { score = 0; } - return score; case NUCLEOTIDE: byte base = centerAlignment.getBase(adjustedCenter); @@ -172,6 +171,10 @@ public double calculateScore(AlignmentTrack.SortOption option, double center, Al //String hapname = centerAlignment.getHaplotypeName(); //return hapname == null ? 0 : hapname.hashCode(); return centerAlignment.getHapDistance(); + case READ_NAME: + String readName = centerAlignment.getReadName(); + score = readName == null ? 0 : readName.hashCode(); + return score; default: return Integer.MAX_VALUE; diff --git a/sv.png b/sv.png deleted file mode 100644 index 7eba186707..0000000000 Binary files a/sv.png and /dev/null differ diff --git a/test.png b/test.png deleted file mode 100644 index 1589279bfa..0000000000 Binary files a/test.png and /dev/null differ