From b5b2401fc95523d93793397a2a185ccccdebb4f7 Mon Sep 17 00:00:00 2001
From: Robert Thurman <rthurman@uw.edu>
Date: Fri, 11 Apr 2014 15:50:46 -0700
Subject: [PATCH] Remove support for jarch in run_add_peaks_per_hotspot.

---
 hotspot-distr/CHANGES                         |  8 ++++++
 .../run_add_peaks_per_hotspot                 | 25 +++++--------------
 2 files changed, 14 insertions(+), 19 deletions(-)

diff --git a/hotspot-distr/CHANGES b/hotspot-distr/CHANGES
index 2d105d4..18f15d4 100644
--- a/hotspot-distr/CHANGES
+++ b/hotspot-distr/CHANGES
@@ -82,3 +82,11 @@ run_badspot
 
 Remove use of /tmp.  All scripts now write temp files "in place" to
 output directories.
+
+
+run_add_peaks_per_hotspot
+-------------------------------------------------------------------
+
+Remove support for jarch density files.  Jarch format has been
+supplanted by starch, and its use triggers 141 exit codes, as
+previously noted.
diff --git a/hotspot-distr/pipeline-scripts/run_add_peaks_per_hotspot b/hotspot-distr/pipeline-scripts/run_add_peaks_per_hotspot
index cd5035a..d572530 100755
--- a/hotspot-distr/pipeline-scripts/run_add_peaks_per_hotspot
+++ b/hotspot-distr/pipeline-scripts/run_add_peaks_per_hotspot
@@ -48,8 +48,6 @@ elif [ -d $dens ]; then
     dens=$dens/$proj.tagdensity.bed.starch
 fi
 
-dentype=${dens##*.}
-
 ## Check genome-wide output.
 pk=$pdir/$proj.peaks.bed
 if [ ! -e $pk ]; then
@@ -107,23 +105,12 @@ do
 	    echo "$thisscr: error: $dens does not exist; run run_wavelet_peak_finding to generate."
 	    exit 1
 	fi
-	if [ $dentype == "jarch" ]; then
-	    gchr $dens \
-		| bedmap --delim ";" --echo-map --max $tmpdom - \
-		| awk 'BEGIN{FS=";"}{max=$NF; i=1; go=1; while(i<NF && go==1){split($i, a, "\t"); if(a[5] == max){print $i; go=0}; i++}}' \
-		| awk -v sz=$halfHSS 'BEGIN {FS="\t";OFS=FS} {d=int(($2+$3)/2); e=d-sz; if ( e < 0 ) { e = 0; } print $1, e, d+sz, $4, int($5)}' \
-		| sort-bed - \
-		| bedops -u - $tout \
-		> $combbed
-	else
-	    ## Density is starch file, or text.
-	    bedmap --delim ";" --echo-map --max $tmpdom $dens \
-		| awk 'BEGIN{FS=";"}{max=$NF; i=1; go=1; while(i<NF && go==1){split($i, a, "\t"); if(a[5] == max){print $i; go=0}; i++}}' \
-		| awk -v sz=$halfHSS 'BEGIN {FS="\t";OFS=FS} {d=int(($2+$3)/2); e=d-sz; if ( e < 0 ) { e = 0; } print $1, e, d+sz, $4, int($5)}' \
-		| sort-bed - \
-		| bedops -u - $tout \
-		> $combbed
-	fi
+	bedmap --delim ";" --echo-map --max $tmpdom $dens \
+	    | awk 'BEGIN{FS=";"}{max=$NF; i=1; go=1; while(i<NF && go==1){split($i, a, "\t"); if(a[5] == max){print $i; go=0}; i++}}' \
+	    | awk -v sz=$halfHSS 'BEGIN {FS="\t";OFS=FS} {d=int(($2+$3)/2); e=d-sz; if ( e < 0 ) { e = 0; } print $1, e, d+sz, $4, int($5)}' \
+	    | sort-bed - \
+	    | bedops -u - $tout \
+	    > $combbed
     fi
 
     echo "track name=$name" > $combwig