Merge branch 'master' of https://github.com/aidenlab/juicer into PBS_fix (968032d4) · Commits · Chaos / chaos.juicer

CPU/juicer.sh

+4 −4

Changes for CPU/juicer.sh: 4 added lines, 4 removed lines.
Original line number	Diff line number	Diff line
		@@ -367,8 +367,8 @@ then
		# Align read1
		if [ -n "$shortread" ] \|\| [ "$shortreadend" -eq 1 ]
		then
		echo "Running command bwa aln -q 15 $refSeq $name1$ext > $name1$ext.sai && bwa samse $refSeq $name1$ext.sai $name1$ext > $name1$ext.sam"
		bwa aln -q 15 $refSeq $name1$ext > $name1$ext.sai && bwa samse $refSeq $name1$ext.sai $name1$ext > $name1$ext.sam
		echo "Running command bwa aln -q 15 $threadstring $refSeq $name1$ext > $name1$ext.sai && bwa samse $refSeq $name1$ext.sai $name1$ext > $name1$ext.sam"
		bwa aln -q 15 $threadstring $refSeq $name1$ext > $name1$ext.sai && bwa samse $refSeq $name1$ext.sai $name1$ext > $name1$ext.sam
		if [ $? -ne 0 ]
		then
		echo "***! Alignment of $name1$ext failed."
		@@ -390,8 +390,8 @@ then
		# Align read2
		if [ -n "$shortread" ] \|\| [ "$shortreadend" -eq 2 ]
		then
		echo "Running command bwa aln -q 15 $refSeq $name2$ext > $name2$ext.sai && bwa samse $refSeq $name2$ext.sai $name2$ext > $name2$ext.sam "
		bwa aln -q 15 $refSeq $name2$ext > $name2$ext.sai && bwa samse $refSeq $name2$ext.sai $name2$ext > $name2$ext.sam
		echo "Running command bwa aln -q 15 $threadstring $refSeq $name2$ext > $name2$ext.sai && bwa samse $refSeq $name2$ext.sai $name2$ext > $name2$ext.sam "
		bwa aln -q 15 $threadstring $refSeq $name2$ext > $name2$ext.sai && bwa samse $refSeq $name2$ext.sai $name2$ext > $name2$ext.sam
		if [ $? -ne 0 ]
		then
		echo "***! Alignment of $name2$ext failed."

+3 −0

Changes for README.md: 3 added lines, 0 removed lines.
Original line number	Diff line number	Diff line
		@@ -17,6 +17,9 @@ Neva C. Durand, Muhammad S. Shamim, Ido Machol, Suhas S. P. Rao, Miriam H. Huntl
		# Documentation
		Please see [the wiki](https://github.com/theaidenlab/juicer/wiki) for extensive documentation.

		# Questions?
		For FAQs, or for asking new questions, please see our forum: [aidenlab.org/forum.html](http://aidenlab.org/forum.html).

		------------
		Distribution
		------------

+1 −1

Changes for misc/calculate_map_resolution.sh: 1 added line, 1 removed line.
Original line number	Diff line number	Diff line
		@@ -97,7 +97,7 @@ threshold=$(( $threshold / 5 ))

		echo -ne "."
		newbin=50
		bins1000=$(awk '$3>=1000{sum++}END{print sum}' $coveragename)
		bins1000=$(awk '$3>=1000{sum++}END{if (sum == 0) print 0; else print sum}' $coveragename)
		lowrange=$newbin

		# find reasonable range with big jumps