From 4c48260fe1d60bd320c8c42c2a1868e106bd268b Mon Sep 17 00:00:00 2001
From: ottojolanki <ojolanki@stanford.edu>
Date: Mon, 16 Dec 2019 09:45:50 -0800
Subject: [PATCH 1/3] update File instead of Array[File] outputs from
 bam_to_signals

---
 .isort.cfg             |  2 +-
 output_definition.json | 20 ++++++++++++++++++--
 2 files changed, 19 insertions(+), 3 deletions(-)

diff --git a/.isort.cfg b/.isort.cfg
index dd54d88..218e3a3 100644
--- a/.isort.cfg
+++ b/.isort.cfg
@@ -3,4 +3,4 @@ multi_line_output=3
 include_trailing_comma=True
 force_grid_wrap=0
 use_parentheses=True
-known_third_party = align,compare_md5,merge_annotation,pandas,pysam,qc_utils,rna_qc,rsem_quant
+known_third_party = compare_md5,merge_annotation,pandas,pysam,qc_utils,rna_qc,rsem_quant
diff --git a/output_definition.json b/output_definition.json
index 2b7e86f..48bd10d 100644
--- a/output_definition.json
+++ b/output_definition.json
@@ -38,7 +38,15 @@
     }
   },
   "rna.bam_to_signals": {
-    "all": {
+    "all_minus": {
+      "path": "bam_to_signals/rep${i+1}/${basename}",
+      "table": "Bam_to_signals/Replicate ${i+1}/signal track of all reads from minus strand"
+    },
+    "all_plus": {
+      "path": "bam_to_signals/rep${i+1}/${basename}",
+      "table": "Bam_to_signals/Replicate ${i+1}/signal track of all reads from plus strand"
+    },
+    "all_unstranded": {
       "path": "bam_to_signals/rep${i+1}/${basename}",
       "table": "Bam_to_signals/Replicate ${i+1}/signal track of all reads"
     },
@@ -46,7 +54,15 @@
       "path": "bam_to_signals/rep${i+1}/${basename}",
       "table": "Bam_to_signals/Replicate ${i+1}/python log"
     },
-    "unique": {
+    "unique_minus": {
+      "path": "bam_to_signals/rep${i+1}/${basename}",
+      "table": "Bam_to_signals/Replicate ${i+1}/signal track of unique reads from minus strand"
+    },
+    "unique_plus": {
+      "path": "bam_to_signals/rep${i+1}/${basename}",
+      "table": "Bam_to_signals/Replicate ${i+1}/signal track of unique reads from plus strand"
+    },
+    "unique_unstranded": {
       "path": "bam_to_signals/rep${i+1}/${basename}",
       "table": "Bam_to_signals/Replicate ${i+1}/signal track of unique reads"
     }

From 6208b23aa6add919e728ac518c6046a86e341e90 Mon Sep 17 00:00:00 2001
From: ottojolanki <ojolanki@stanford.edu>
Date: Mon, 16 Dec 2019 13:03:30 -0800
Subject: [PATCH 2/3] turn autoscale and smoothing window off

---
 output_definition.json | 18 ++++++++++++------
 1 file changed, 12 insertions(+), 6 deletions(-)

diff --git a/output_definition.json b/output_definition.json
index 48bd10d..0607cdc 100644
--- a/output_definition.json
+++ b/output_definition.json
@@ -40,15 +40,18 @@
   "rna.bam_to_signals": {
     "all_minus": {
       "path": "bam_to_signals/rep${i+1}/${basename}",
-      "table": "Bam_to_signals/Replicate ${i+1}/signal track of all reads from minus strand"
+      "table": "Bam_to_signals/Replicate ${i+1}/signal track of all reads from minus strand",
+      "ucsc_track": "track type=bigWig name=\"rep${i+1} all minus\" priority=${i+1} visibility=full smoothingWindow=off autoScale=off"
     },
     "all_plus": {
       "path": "bam_to_signals/rep${i+1}/${basename}",
-      "table": "Bam_to_signals/Replicate ${i+1}/signal track of all reads from plus strand"
+      "table": "Bam_to_signals/Replicate ${i+1}/signal track of all reads from plus strand",
+      "ucsc_track": "track type=bigWig name=\"rep${i+1} all plus\" priority=${i+1} visibility=full smoothingWindow=off autoScale=off"
     },
     "all_unstranded": {
       "path": "bam_to_signals/rep${i+1}/${basename}",
-      "table": "Bam_to_signals/Replicate ${i+1}/signal track of all reads"
+      "table": "Bam_to_signals/Replicate ${i+1}/signal track of all reads",
+      "ucsc_track": "track type=bigWig name=\"rep${i+1} all\" priority=${i+1} visibility=full smoothingWindow=off autoScale=off"
     },
     "python_log": {
       "path": "bam_to_signals/rep${i+1}/${basename}",
@@ -56,15 +59,18 @@
     },
     "unique_minus": {
       "path": "bam_to_signals/rep${i+1}/${basename}",
-      "table": "Bam_to_signals/Replicate ${i+1}/signal track of unique reads from minus strand"
+      "table": "Bam_to_signals/Replicate ${i+1}/signal track of unique reads from minus strand",
+      "ucsc_track": "track type=bigWig name=\"rep${i+1} unique minus\" priority=${i+1} visibility=full smoothingWindow=off autoScale=off"
     },
     "unique_plus": {
       "path": "bam_to_signals/rep${i+1}/${basename}",
-      "table": "Bam_to_signals/Replicate ${i+1}/signal track of unique reads from plus strand"
+      "table": "Bam_to_signals/Replicate ${i+1}/signal track of unique reads from plus strand",
+      "ucsc_track": "track type=bigWig name=\"rep${i+1} unique plus\" priority=${i+1} visibility=full smoothingWindow=off autoScale=off"
     },
     "unique_unstranded": {
       "path": "bam_to_signals/rep${i+1}/${basename}",
-      "table": "Bam_to_signals/Replicate ${i+1}/signal track of unique reads"
+      "table": "Bam_to_signals/Replicate ${i+1}/signal track of unique reads",
+      "ucsc_track": "track type=bigWig name=\"rep${i+1} unique\" priority=${i+1} visibility=full smoothingWindow=off autoScale=off"
     }
   },
   "rna.kallisto": {

From 1de366badf2641dd1f246869aab3c2c5f53e82ff Mon Sep 17 00:00:00 2001
From: ottojolanki <ojolanki@stanford.edu>
Date: Mon, 16 Dec 2019 14:05:07 -0800
Subject: [PATCH 3/3] track settings that match the ones from portal added

---
 output_definition.json | 12 ++++++------
 1 file changed, 6 insertions(+), 6 deletions(-)

diff --git a/output_definition.json b/output_definition.json
index 0607cdc..90ae64e 100644
--- a/output_definition.json
+++ b/output_definition.json
@@ -41,17 +41,17 @@
     "all_minus": {
       "path": "bam_to_signals/rep${i+1}/${basename}",
       "table": "Bam_to_signals/Replicate ${i+1}/signal track of all reads from minus strand",
-      "ucsc_track": "track type=bigWig name=\"rep${i+1} all minus\" priority=${i+1} visibility=full smoothingWindow=off autoScale=off"
+      "ucsc_track": "track type=bigWig name=\"rep${i+1} all minus\" priority=${i+1} visibility=full smoothingWindow=off windowingFunction=mean+whiskers autoScale=off negateValues=on viewLimits=-1:0 transformFunc=LOG maxHeightPixels=64:18:8"
     },
     "all_plus": {
       "path": "bam_to_signals/rep${i+1}/${basename}",
       "table": "Bam_to_signals/Replicate ${i+1}/signal track of all reads from plus strand",
-      "ucsc_track": "track type=bigWig name=\"rep${i+1} all plus\" priority=${i+1} visibility=full smoothingWindow=off autoScale=off"
+      "ucsc_track": "track type=bigWig name=\"rep${i+1} all plus\" priority=${i+1} visibility=full smoothingWindow=off windowingFunction=mean+whiskers autoScale=off viewLimits=0:1 transformFunc=LOG maxHeightPixels=64:18:8"
     },
     "all_unstranded": {
       "path": "bam_to_signals/rep${i+1}/${basename}",
       "table": "Bam_to_signals/Replicate ${i+1}/signal track of all reads",
-      "ucsc_track": "track type=bigWig name=\"rep${i+1} all\" priority=${i+1} visibility=full smoothingWindow=off autoScale=off"
+      "ucsc_track": "track type=bigWig name=\"rep${i+1} all\" priority=${i+1} visibility=full smoothingWindow=off windowingFunction=mean+whiskers autoScale=off viewLimits=0:1 transformFunc=LOG maxHeightPixels=64:18:8"
     },
     "python_log": {
       "path": "bam_to_signals/rep${i+1}/${basename}",
@@ -60,17 +60,17 @@
     "unique_minus": {
       "path": "bam_to_signals/rep${i+1}/${basename}",
       "table": "Bam_to_signals/Replicate ${i+1}/signal track of unique reads from minus strand",
-      "ucsc_track": "track type=bigWig name=\"rep${i+1} unique minus\" priority=${i+1} visibility=full smoothingWindow=off autoScale=off"
+      "ucsc_track": "track type=bigWig name=\"rep${i+1} unique minus\" priority=${i+1} visibility=full smoothingWindow=off windowingFunction=mean+whiskers autoScale=off negateValues=on viewLimits=-1:0 transformFunc=LOG maxHeightPixels=64:18:8"
     },
     "unique_plus": {
       "path": "bam_to_signals/rep${i+1}/${basename}",
       "table": "Bam_to_signals/Replicate ${i+1}/signal track of unique reads from plus strand",
-      "ucsc_track": "track type=bigWig name=\"rep${i+1} unique plus\" priority=${i+1} visibility=full smoothingWindow=off autoScale=off"
+      "ucsc_track": "track type=bigWig name=\"rep${i+1} unique plus\" priority=${i+1} visibility=full smoothingWindow=off windowingFunction=mean+whiskers autoScale=off viewLimits=0:1 transformFunc=LOG maxHeightPixels=64:18:8"
     },
     "unique_unstranded": {
       "path": "bam_to_signals/rep${i+1}/${basename}",
       "table": "Bam_to_signals/Replicate ${i+1}/signal track of unique reads",
-      "ucsc_track": "track type=bigWig name=\"rep${i+1} unique\" priority=${i+1} visibility=full smoothingWindow=off autoScale=off"
+      "ucsc_track": "track type=bigWig name=\"rep${i+1} unique\" priority=${i+1} visibility=full smoothingWindow=off windowingFunction=mean+whiskers autoScale=off viewLimits=0:1 transformFunc=LOG maxHeightPixels=64:18:8"
     }
   },
   "rna.kallisto": {