define( [
    'JBrowse/Util'
],
function(Util) {

var c = {
    colorAlignment(feature, score, glyph, track) {
        var strand = feature.get('strand');
        if (Math.abs(strand) != 1 && strand != '+' && strand != '-') {
            return track.colorForBase('reference');
        } else if (track.config.colorByOrientationAndSize) {
            return c.colorByOrientationAndSize.apply(null, arguments)
        } else if (track.config.colorByOrientation) {
            return c.colorByOrientation.apply(null, arguments)
        } else if (track.config.colorBySize) {
            return c.colorByInsertSizePercentile.apply(null, arguments)
        } else if (track.config.useXS) {
            return c.colorByXS.apply(null, arguments)
        } else if (track.config.useTS) {
            return c.colorByTS.apply(null, arguments)
        } else if (track.config.colorByMAPQ) {
            return c.colorByMAPQ.apply(null, arguments)
        } else if (track.config.defaultColor||track.config.useReverseTemplate) {
            if(feature.get('multi_segment_template')) {
                var revflag = feature.get('multi_segment_first');
                if (feature.get('multi_segment_all_correctly_aligned')) {
                    if (revflag || !track.config.useReverseTemplate) {
                        return strand == 1 || strand == '+'
                              ? glyph.getStyle( feature, 'color_fwd_strand' )
                              : glyph.getStyle( feature, 'color_rev_strand' );
                    } else {
                        return strand == 1 || strand == '+'
                            ? glyph.getStyle( feature, 'color_rev_strand' )
                            : glyph.getStyle( feature, 'color_fwd_strand' );
                    }
                }
                if (feature.get('multi_segment_next_segment_unmapped')) {
                    if (revflag || !track.config.useReverseTemplate) {
                        return strand == 1 || strand == '+'
                              ? glyph.getStyle( feature, 'color_fwd_missing_mate' )
                              : glyph.getStyle( feature, 'color_rev_missing_mate' );
                    } else{
                        return strand == 1 || strand == '+'
                              ? glyph.getStyle( feature, 'color_rev_missing_mate' )
                              : glyph.getStyle( feature, 'color_fwd_missing_mate' );
                    }
                }
                if (feature.get('seq_id') == feature.get('next_seq_id')) {
                    if (revflag || !track.config.useReverseTemplate) {
                        return strand == 1 || strand == '+'
                              ? glyph.getStyle( feature, 'color_fwd_strand_not_proper' )
                              : glyph.getStyle( feature, 'color_rev_strand_not_proper' );
                    } else {
                        return strand == 1 || strand == '+'
                              ? glyph.getStyle( feature, 'color_rev_strand_not_proper' )
                              : glyph.getStyle( feature, 'color_fwd_strand_not_proper' );
                    }
                }
                // should only leave aberrant chr
                return strand == 1 || strand == '+'
                        ? glyph.getStyle( feature, 'color_fwd_diff_chr' )
                        : glyph.getStyle( feature, 'color_rev_diff_chr' );
            }
            return strand == 1 || strand == '+'
                  ? glyph.getStyle( feature, 'color_fwd_strand' )
                  : glyph.getStyle( feature, 'color_rev_strand' );
        }
        else return glyph.getStyle( feature, 'color_nostrand' )
    },

    getOrientation(feature, score, glyph, track)  {
        const type = Util.orientationTypes[track.config.orientationType]
        const orientation = type[feature.get('pair_orientation')]
        const map = {
            'LR': 'color_pair_lr',
            'RR': 'color_pair_rr',
            'RL': 'color_pair_rl',
            'LL': 'color_pair_ll'
        }
        return map[orientation]
    },

    colorByOrientation(feature, score, glyph, track)  {
        const p = c.getOrientation.apply(null, arguments)
        return glyph.getStyle(feature, p || 'color_nostrand')
    },

    colorByOrientationAndSize(feature, score, glyph, track)  {
        const p = c.getInsertSizePercentile.apply(null, arguments)
        if(!p) {
            return c.colorByOrientation.apply(null, arguments)
        }
        return glyph.getStyle(feature, p)
    },
    getInsertSizePercentile(feature, score, glyph, track) {
        if (feature.get('is_paired')) {
            const len = Math.abs(feature.get('template_length'))
            if(feature.get('seq_id') != feature.get('next_seq_id')) {
                return 'color_interchrom'
            } else if (track.insertSizeStats.upper < len) {
                return 'color_longinsert'
            } else if (track.insertSizeStats.lower > len) {
                return 'color_shortinsert'
            }
        }
        return null
    },
    colorByInsertSizePercentile(feature, score, glyph, track) {
        const p = c.getInsertSizePercentile.apply(null, arguments)
        return glyph.getStyle(feature, p || 'color_nostrand')
    },

    colorByInsertSize(feature, score, glyph, track) {
        if (feature.get('is_paired') && feature.get('seq_id') != feature.get('next_seq_id')) {
            return glyph.getStyle(feature, 'color_interchrom')
        }
        const s = Math.abs(score/10)
        return `hsl(${s},50%,50%)`;
    },

    colorArcs(feature, score, glyph, track) {
        if (track.config.colorByOrientationAndSize) {
            return c.colorByOrientationAndSize.apply(null, arguments)
        } else if (track.config.colorBySize) {
            return c.colorByInsertSizePercentile.apply(null, arguments)
        } else if (track.config.colorByOrientation) {
            return c.colorByOrientation.apply(null, arguments)
        } else if (track.config.colorByMAPQ) {
            return c.colorByMAPQ.apply(null, arguments)
        } else {
            return c.colorByInsertSize.apply(null, arguments)
        }
    },

    connectorColor(feature, score, glyph, track) {
        if (track.config.colorByOrientation) {
            return c.colorByOrientation.apply(null, arguments)
        } else if(track.config.colorByOrientationAndSize) {
            return c.colorByOrientationAndSize.apply(null, arguments)
        } else {
            return 'black'
        }
    },

    colorByXS(feature, score, glyph, track) {
        const map = {
            '-': 'color_rev_strand',
            '+': 'color_fwd_strand'
        };
        return glyph.getStyle(feature, map[feature.get('xs')] || 'color_nostrand');
    },

    // TS is flipped from XS
    colorByTS(feature, score, glyph, track) {
        const map = {
            '-': feature.get('strand') === -1 ? 'color_fwd_strand' : 'color_rev_strand',
            '+': feature.get('strand') === -1 ? 'color_rev_strand' : 'color_fwd_strand'
        }
        return glyph.getStyle(feature, map[feature.get('ts')] || 'color_nostrand');
    },

    // assumes score cap at 60, which is used by bwa-mem and other tools. some cap at 37
    colorByMAPQ(feature, score, glyph, track) {
        const c = Math.min(feature.get('score') * 4, 200)
        return `rgb(${c},${c},${c})`;
    }
};

return c;

});

@@ -6673,16 +6673,57 @@
      %7D;%0A
+        console.log(feature.get('tags'))%0A
         
@@ -6774,16 +6774,40 @@
 et('xs')
+%7C%7Cfeature.get('tags').XS
 %5D %7C%7C 'co
@@ -7174,16 +7174,40 @@
 et('ts')
+%7C%7Cfeature.get('tags').TS
 %5D %7C%7C 'co

Add check for CRAM tags