diff --git a/CHANGELOG.md b/CHANGELOG.md
index 39ad52a5dad8332451ef7a68cf2fa1ce902646f6..6c7922a1f6b2c36bfd3c2cf9ab81461ef56c6d7a 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -1,10 +1,9 @@
# nf-core/hic: Changelog
-
## v1.1dev
+* Add --saveInteractionBAM option
* Fix bug for reads extension _1/_2 (#30)
-
* Update manual (#28)
## v1.0 - 2019-05-06
diff --git a/bin/mapped_2hic_fragments.py b/bin/mapped_2hic_fragments.py
index efa32e6d681c6fc1cbf60843bc588f1371de30f1..d4790ee3114a071cff3131543159d9124bbab1c6 100755
--- a/bin/mapped_2hic_fragments.py
+++ b/bin/mapped_2hic_fragments.py
@@ -53,7 +53,7 @@ def get_args():
"minInsertSize=", "maxInsertSize",
"minFragSize", "maxFragSize",
"minDist",
- "gatg", "samOut", "verbose", "all", "help"])
+ "gatg", "sam", "verbose", "all", "help"])
except getopt.GetoptError:
usage()
sys.exit(-1)
@@ -442,7 +442,7 @@ def get_interaction_type(read1, read1_chrom, resfrag1, read2,
# If returned InteractionType=None -> Same restriction fragment
# and same strand = Dump
interactionType = None
-
+
if not read1.is_unmapped and not read2.is_unmapped and resfrag1 is not None and resfrag2 is not None:
# same restriction fragment
if resfrag1 == resfrag2:
@@ -501,9 +501,9 @@ if __name__ == "__main__":
minInsertSize = arg
elif opt in ("-l", "--longestInsertSize"):
maxInsertSize = arg
- elif opt in ("-t", "--shortestFragmentSize"):
+ elif opt in ("-t", "--shortestFragmentLength"):
minFragSize = arg
- elif opt in ("-m", "--longestFragmentSize"):
+ elif opt in ("-m", "--longestFragmentLength"):
maxFragSize = arg
elif opt in ("-d", "--minCisDist"):
minDist = arg
@@ -613,6 +613,7 @@ if __name__ == "__main__":
r2_chrom = None
if r1_resfrag is not None or r2_resfrag is not None:
+
interactionType = get_interaction_type(r1, r1_chrom, r1_resfrag, r2, r2_chrom, r2_resfrag, verbose)
dist = get_PE_fragment_size(r1, r2, r1_resfrag, r2_resfrag, interactionType)
cdist = get_cis_dist(r1, r2)
@@ -724,10 +725,14 @@ if __name__ == "__main__":
if or1_resfrag is not None:
or1_fragname = or1_resfrag.value['name']
-
+ else:
+ or1_fragname = 'None'
+
if or2_resfrag is not None:
or2_fragname = or2_resfrag.value['name']
-
+ else:
+ or2_fragname = 'None'
+
cur_handler.write(
or1.qname + "\t" +
or1_chrom + "\t" +
diff --git a/conf/hicpro.config b/conf/hicpro.config
index 0a2c9b9e0db09f4f9861ba353b84a534820aba38..01b755a955c5aee521a6cf43b00847cfbc8d0cd3 100644
--- a/conf/hicpro.config
+++ b/conf/hicpro.config
@@ -38,5 +38,6 @@ params {
saveReference = false
saveAlignedIntermediates = false
+ saveInteractionBAM = false
}
diff --git a/main.nf b/main.nf
index 1bd5a3a821f01b05887aa3dc1fefbee47a58fc34..31f73a8549e76b246fe05981c0c2735b5605090e 100644
--- a/main.nf
+++ b/main.nf
@@ -32,6 +32,8 @@ def helpMessage() {
--fasta Path to Fasta reference
--chromosome_size Path to chromosome size file
--restriction_fragments Path to restriction fragment file (bed)
+ --saveReference Save reference genome to output folder. Default: False
+ --saveAlignedIntermediates Save intermediates alignment files. Default: False
Options:
--bwt2_opts_end2end Options for bowtie2 end-to-end mappinf (first mapping step). See hic.config for default.
@@ -43,8 +45,9 @@ def helpMessage() {
--max_restriction_framgnet_size Maximum size of restriction fragmants to consider. Default: None
--min_insert_size Minimum insert size of mapped reads to consider. Default: None
--max_insert_size Maximum insert size of mapped reads to consider. Default: None
+ --saveInteractionBAM Save BAM file with interaction tags (dangling-end, self-circle, etc.). Default: False
- --dnase Run DNase Hi-C mode. All options related to restriction fragments are not considered. Default: false
+ --dnase Run DNase Hi-C mode. All options related to restriction fragments are not considered. Default: False
--min_cis_dist Minimum intra-chromosomal distance to consider. Default: None
--rm_singleton Remove singleton reads. Default: true
@@ -65,10 +68,10 @@ def helpMessage() {
Step options:
- --skip_maps Skip generation of contact maps. Useful for capture-C. Default: false
- --skip_ice Skip ICE normalization. Default: false
- --skip_cool Skip generation of cool files. Default: false
- --skip_multiQC Skip MultiQC. Default: false
+ --skip_maps Skip generation of contact maps. Useful for capture-C. Default: False
+ --skip_ice Skip ICE normalization. Default: False
+ --skip_cool Skip generation of cool files. Default: False
+ --skip_multiQC Skip MultiQC. Default: False
AWSBatch options:
--awsqueue The AWSBatch JobQueue that needs to be set when running on AWSBatch
@@ -154,7 +157,7 @@ if ( params.splitFastq ){
raw_reads_full = raw_reads.concat( raw_reads_2 )
raw_reads = raw_reads_full.splitFastq( by: params.splitFastq , file: true)
}else{
- raw_reads = raw_reads.concat( raw_reads_2 )
+ raw_reads = raw_reads.concat( raw_reads_2 ).dump(tag: "data")
}
@@ -599,6 +602,10 @@ if (!params.dnase){
output:
set val(sample), file("*.validPairs") into valid_pairs
set val(sample), file("*.validPairs") into valid_pairs_4cool
+ set val(sample), file("*.DEPairs") into de_pairs
+ set val(sample), file("*.SCPairs") into sc_pairs
+ set val(sample), file("*.REPairs") into re_pairs
+ set val(sample), file("*.FiltPairs") into filt_pairs
set val(sample), file("*RSstat") into all_rsstat
script:
@@ -612,9 +619,10 @@ if (!params.dnase){
if ("$params.max_insert_size".isInteger()) opts="${opts} -l ${params.max_insert_size}"
if ("$params.min_restriction_fragment_size".isInteger()) opts="${opts} -t ${params.min_restriction_fragment_size}"
if ("$params.max_restriction_fragment_size".isInteger()) opts="${opts} -m ${params.max_restriction_fragment_size}"
+ if (params.saveInteractionBAM) opts="${opts} --sam"
"""
- mapped_2hic_fragments.py -f ${frag_file} -r ${pe_bam} ${opts}
+ mapped_2hic_fragments.py -f ${frag_file} -r ${pe_bam} --all ${opts}
"""
}
}