Add base modification options to alignment track preferences (defaults)

igvteam · Mar 24, 2024 · 00cd2db · 00cd2db
1 parent 33d97c8
commit 00cd2db
Showing 1 changed file with 2 additions and 2 deletions.
diff --git a/src/main/resources/org/broad/igv/prefs/preferences.tab b/src/main/resources/org/broad/igv/prefs/preferences.tab
@@ -102,9 +102,9 @@ SAM.MAX_LEVELS	Number of reads per window	integer	100
 SAM.ALLELE_THRESHOLD	Coverage allele-fraction threshold	float	0.2
 SAM.ALLELE_USE_QUALITY	Quality weight allele fraction	boolean	TRUE
 
-##Alignment Track Options
+##Alignment Track Defaults
 
-SAM.COLOR_BY	Color alignments by	select NONE|READ_STRAND|FIRST_OF_PAIR_STRAND|PAIR_ORIENTATION|UNEXPECTED_PAIR|INSERT_SIZE|SAMPLE|READ_GROUP|LIBRARY|MOVIE|ZMW|BISULFITE|NOMESEQ|TAG|MAPPED_SIZE|LINK_STRAND|YC_TAG	UNEXPECTED_PAIR
+SAM.COLOR_BY	Color alignments by	select NONE|READ_STRAND|FIRST_OF_PAIR_STRAND|PAIR_ORIENTATION|UNEXPECTED_PAIR|INSERT_SIZE|BASE_MODIFICATION|BASE_MODIFICATION_2COLOR|SAMPLE|READ_GROUP|LIBRARY|MOVIE|ZMW|BISULFITE|NOMESEQ|TAG|MAPPED_SIZE|LINK_STRAND|YC_TAG	UNEXPECTED_PAIR
 SAM.COLOR_BY_TAG	Color by TAG	string
 SAM.GROUP_OPTION	Group alignments by	select NONE|STRAND|SAMPLE|READ_GROUP|LIBRARY|FIRST_OF_PAIR_STRAND|TAG|PAIR_ORIENTATION|MATE_CHROMOSOME|SV_ALIGNMENT|SUPPLEMENTARY|BASE_AT_POS|MOVIE|ZMW|HAPLOTYPE|READ_ORDER|LINKED|PHASE|MAPPING_QUALITY
 SAM.GROUP_BY_TAG	Group by TAG	string