Merge branch 'master' of https://github.com/jbelyeu/samplot

Author: jbelyeu

README.md

@@ -16,27 +16,8 @@ substantiate the SV.
   <summary>samplot plot</summary>
 
   ```
-usage: samplot plot [-h] [--marker_size MARKER_SIZE] [-n TITLES [TITLES ...]]
-                    [-r REFERENCE] [-z Z] -b BAMS [BAMS ...] -o OUTPUT_FILE -s
-                    START -e END -c CHROM [-w WINDOW] [-d MAX_DEPTH]
-                    [--minq MINQ] [-t SV_TYPE] [-T TRANSCRIPT_FILE]
-                    [-A ANNOTATION_FILES [ANNOTATION_FILES ...]]
-                    [--coverage_tracktype {stack,superimpose}] [-a]
-                    [-H PLOT_HEIGHT] [-W PLOT_WIDTH] [-q MIN_MQUAL] [-j]
-                    [--start_ci START_CI] [--end_ci END_CI]
-                    [--long_read LONG_READ] [--min_event_size MIN_EVENT_SIZE]
-                    [--xaxis_label_fontsize XAXIS_LABEL_FONTSIZE]
-                    [--yaxis_label_fontsize YAXIS_LABEL_FONTSIZE]
-                    [--legend_fontsize LEGEND_FONTSIZE]
-                    [--annotation_fontsize ANNOTATION_FONTSIZE]
-                    [--common_insert_size] [--hide_annotation_labels]
-                    [--coverage_only] [--same_yaxis_scales] [--zoom ZOOM]
-                    [--debug DEBUG]
-
 optional arguments:
   -h, --help            show this help message and exit
-  --marker_size MARKER_SIZE
-                        Size of marks on pairs and splits (default 3)
   -n TITLES [TITLES ...], --titles TITLES [TITLES ...]
                         Space-delimited list of plot titles. Use quote marks
                         to include spaces (i.e. "plot 1" "plot 2")
@@ -46,36 +27,53 @@ optional arguments:
   -b BAMS [BAMS ...], --bams BAMS [BAMS ...]
                         Space-delimited list of BAM/CRAM file names
   -o OUTPUT_FILE, --output_file OUTPUT_FILE
-                        Output file name
+                        Output file name/type. Defaults to
+                        {type}_{chrom}_{start}_{end}.png
+  --output_dir OUTPUT_DIR
+                        Output directory name. Defaults to working dir.
+                        Ignored if --output_file is set
   -s START, --start START
-                        Start position of region/variant
-  -e END, --end END     End position of region/variant
+                        Start position of region/variant (add multiple for
+                        translocation/BND events)
+  -e END, --end END     End position of region/variant (add multiple for
+                        translocation/BND events)
   -c CHROM, --chrom CHROM
-                        Chromosome
+                        Chromosome (add multiple for translocation/BND events)
   -w WINDOW, --window WINDOW
                         Window size (count of bases to include in view),
                         default(0.5 * len)
   -d MAX_DEPTH, --max_depth MAX_DEPTH
                         Max number of normal pairs to plot
-  --minq MINQ           coverage from reads with MAPQ <= minq plotted in
-                        lighter grey. To disable, pass in negative value
   -t SV_TYPE, --sv_type SV_TYPE
                         SV type. If omitted, plot is created without variant
                         bar
   -T TRANSCRIPT_FILE, --transcript_file TRANSCRIPT_FILE
-                        GFF of transcripts
+                        GFF3 of transcripts
+  --transcript_filename TRANSCRIPT_FILENAME
+                        Name for transcript track
+  --max_coverage_points MAX_COVERAGE_POINTS
+                        number of points to plot in coverage axis (downsampled
+                        from region size for speed)
   -A ANNOTATION_FILES [ANNOTATION_FILES ...], --annotation_files ANNOTATION_FILES [ANNOTATION_FILES ...]
                         Space-delimited list of bed.gz tabixed files of
                         annotations (such as repeats, mappability, etc.)
-  --coverage_tracktype {stack,superimpose}
+  --annotation_filenames ANNOTATION_FILENAMES [ANNOTATION_FILENAMES ...]
+                        Space-delimited list of names for the tracks in
+                        --annotation_files
+  --coverage_tracktype {stack,superimpose,none}
                         type of track to use for low MAPQ coverage plot.
   -a, --print_args      Print commandline arguments
   -H PLOT_HEIGHT, --plot_height PLOT_HEIGHT
                         Plot height
   -W PLOT_WIDTH, --plot_width PLOT_WIDTH
                         Plot width
-  -q MIN_MQUAL, --min_mqual MIN_MQUAL
+  -q INCLUDE_MQUAL, --include_mqual INCLUDE_MQUAL
                         Min mapping quality of reads to be included in plot
+                        (default 1)
+  --separate_mqual SEPARATE_MQUAL
+                        coverage from reads with MAPQ <= separate_mqual
+                        plotted in lighter grey. To disable, pass in negative
+                        value
   -j, --json_only       Create only the json file, not the image plot
   --start_ci START_CI   confidence intervals of SV first breakpoint (distance
                         from the breakpoint). Must be a comma-separated pair
@@ -86,9 +84,10 @@ optional arguments:
   --long_read LONG_READ
                         Min length of a read to be treated as a long-read
                         (default 1000)
+  --ignore_hp           Choose to ignore HP tag in alignment files
   --min_event_size MIN_EVENT_SIZE
                         Min size of an event in long-read CIGAR to include
-                        (default 100)
+                        (default 20)
   --xaxis_label_fontsize XAXIS_LABEL_FONTSIZE
                         Font size for X-axis labels (default 6)
   --yaxis_label_fontsize YAXIS_LABEL_FONTSIZE
@@ -100,10 +99,17 @@ optional arguments:
   --common_insert_size  Set common insert size for all plots
   --hide_annotation_labels
                         Hide the label (fourth column text) from annotation
-                        files, useful for region with many annotations
+                        files, useful for regions with many annotations
   --coverage_only       Hide all reads and show only coverage
+  --max_coverage MAX_COVERAGE
+                        apply a maximum coverage cutoff. Unlimited by default
   --same_yaxis_scales   Set the scales of the Y axes to the max of all
-  --zoom ZOOM           Only show +- zoom amount around breakpoints
+  --marker_size MARKER_SIZE
+                        Size of marks on pairs and splits (default 3)
+  --dpi DPI             Dots per inches (pixel count, default 300)
+  --zoom ZOOM           Only show +- zoom amount around breakpoints, much
+                        faster for large regions. Ignored if region smaller
+                        than --zoom (default 500000)
   --debug DEBUG         Print debug statements
 ```
 </details>