Merge pull request #52 from yhoogstrate/breakpoint_entropy

Breakpoint entropy

Changelog

@@ -1,3 +1,7 @@
+2017-04-12	Youri Hoogstrate	v0.6.0
+	* Changed behavior of pruning: less post-merging steps necessary
+	* Added two extra variables that can be used for classification
+
 2017-04-05	Youri Hoogstrate	v0.5.0
 	* Large improvements in parsing junctions from reads and much better
 	  performance on circRNAs

drdisco/IntronDecomposition.py

@@ -87,6 +87,15 @@ def merge_frequency_tables(frequency_tables):
     return new_frequency_table
 
 
+def list_to_freq_table(as_list):
+    table = {}
+    for val in as_list:
+        if val not in table:
+            table[val] = 0
+        table[val] += 1
+    return table
+
+
 def bam_parse_alignment_offset(cigartuple):
     pos = 0
     for chunk in cigartuple:
@@ -384,7 +393,11 @@ def __init__(self, _origin, _target):
         self._types = {}
         self._unique_alignment_hashes = {}  # Used for determining entropy
 
-    def get_entropy(self):
+        #  Used for determining entropy / rmsqd:
+        self._unique_breakpoints = {True: ({}, {}),  # discordant mates: (origin , target)
+                                    False: ({}, {})}  # other types: (origin, target)
+
+    def get_entropy_of_alignments(self):
         """Entropy is an important metric / propery of an edge
         The assumption is that all reads should be 'different', i.e.
         have a different start position, different end position,
@@ -438,6 +451,35 @@ def get_entropy(self):
 
         return entropy(self._unique_alignment_hashes)
 
+    def get_distances_to_breakpoints(self, distances_of_discordant_mates):
+        """
+         In the following case all (non-disco) breakpoints are nearly identical:
+
+          [==========> |
+            [========> |
+           [=========> |
+          [==========> |
+           [=========> |
+
+         and here quite variable:
+
+          [=========>   |
+            [=======>   |
+           [=========>  |
+          [===========> |
+           [==========> |
+
+        Here we return the dist to the median of each of the values (0,0,0,0,0) for top example, (-1, -1, 0, 2, 2) for bottom
+        """
+
+        medians = (self._origin.position.pos, self._target.position.pos)
+        dists = []
+        for i in [0, 1]:
+            for key in self._unique_breakpoints[distances_of_discordant_mates][i]:
+                dists += self._unique_breakpoints[distances_of_discordant_mates][i][key] * [medians[i] - key]
+
+        return dists
+
     def get_complement(self):
         try:
             return self._target.edges[self._origin.position._hash]
@@ -450,6 +492,16 @@ def merge_edge(self, edge):
         for alignment_key in edge._unique_alignment_hashes:
             self.add_alignment_key(alignment_key)
 
+        def update_pos(pos, i, is_discordant_mates, n):
+            if pos not in self._unique_breakpoints[is_discordant_mates][i]:
+                self._unique_breakpoints[is_discordant_mates][i][pos] = 0
+            self._unique_breakpoints[is_discordant_mates][i][pos] += n
+
+        for key in [True, False]:
+            for i in [0, 1]:
+                for breakpoint in edge._unique_breakpoints[key][i]:
+                    update_pos(breakpoint, i, key, edge._unique_breakpoints[key][i][breakpoint])
+
         for _type in edge._types:
             if _type != JunctionTypes.silent_mate:
                 self.add_type(_type, edge._types[_type])
@@ -466,6 +518,16 @@ def add_alignment_key(self, alignment_key):
         else:
             self._unique_alignment_hashes[alignment_key] = 1
 
+    def add_break_pos(self, pos1, pos2, is_discordant_mates):
+        def update_pos(pos, i):
+            if pos not in self._unique_breakpoints[is_discordant_mates][i]:
+                self._unique_breakpoints[is_discordant_mates][i][pos] = 1
+            else:
+                self._unique_breakpoints[is_discordant_mates][i][pos] += 1
+
+        update_pos(pos1.pos, 0)
+        update_pos(pos2.pos, 1)
+
     def get_count(self, _type):
         if _type in self._types:
             return self._types[_type]
@@ -576,8 +638,9 @@ def insert_edge(self, pos1, pos2, _type, cigarstrs):
             node2.insert_edge(edge)
 
         edge.add_type(_type, 1)
-        if node1 == edge._origin:  # Avoid double insertion of all keys :) only do it if the positions don't get swapped
+        if node1 == edge._origin and _type != JunctionTypes.cigar_splice_junction:  # Avoid double insertion of all keys :) only do it if the positions don't get swapped
             edge.add_alignment_key(cigarstrs)
+            edge.add_break_pos(pos1, pos2, (_type == JunctionTypes.discordant_mates))
 
     def reinsert_edges(self, edges):
         """Only works for Edges of which the _origin and _target Node
@@ -657,7 +720,7 @@ def prune(self):
         return candidates
 
     def prune_edge(self, edge):
-        #  # @ todo double check if this is strand specific
+        #  @todo double check if this is strand specific
 
         for edge_m in self.search_edges_between(edge):
             d1 = edge._origin.position.get_dist(edge_m._origin.position, True)
@@ -674,8 +737,10 @@ def search_edges_between(self, edge_to_prune):
         """searches for other junctions in-between edge+insert size:"""
         def pos_to_range(pos):
             if pos.strand == STRAND_REVERSE:
-                return (pos.pos - MAX_ACCEPTABLE_INSERT_SIZE) - 1, pos.pos + MAX_ACCEPTABLE_ALIGNMENT_ERROR
+                #  return (pos.pos - MAX_ACCEPTABLE_INSERT_SIZE) - 1, pos.pos + MAX_ACCEPTABLE_ALIGNMENT_ERROR
+                return (pos.pos - MAX_ACCEPTABLE_INSERT_SIZE) - 1, pos.pos + MAX_ACCEPTABLE_INSERT_SIZE
             else:
+                #  return pos.pos - MAX_ACCEPTABLE_ALIGNMENT_ERROR, (pos.pos + MAX_ACCEPTABLE_INSERT_SIZE) + 1
                 return pos.pos - MAX_ACCEPTABLE_ALIGNMENT_ERROR, (pos.pos + MAX_ACCEPTABLE_INSERT_SIZE) + 1
 
         pos1, pos2 = edge_to_prune._origin.position, edge_to_prune._target.position
@@ -876,6 +941,29 @@ def classify_intronic_exonic(self, splice_junctions):
                         return self.xonic
         self.xonic = 2
 
+    def get_breakpoint_stddev(self):
+        """ Calculates the variance of the breakpoints post merge - low values indicate consistent results"""
+        sq_dists = 0.0
+        n = 0
+        for edge in self.edges:
+            for dist in edge.get_distances_to_breakpoints(False):
+                sq_dists += dist ** 2
+                # dist * dist ? math.pow(dist,2)?
+                n += 1
+        if n > 0:
+            return math.sqrt(sq_dists / float(n))
+        else:
+            return 0.0
+
+    def get_breakpoint_disco_entropy(self):
+        """ Calculates the variance of the breakpoints post merge - low values indicate consistent results"""
+        as_list = []
+
+        for edge in self.edges:
+            as_list += edge.get_distances_to_breakpoints(True)
+
+        return entropy(list_to_freq_table(as_list))
+
     def __str__(self):
         """Makes tabular output"""
         node_a, node_b = self.edges[0]._origin, self.edges[0]._target
@@ -891,14 +979,16 @@ def __str__(self):
             "%i\t%i\t%i\t%i\t"
             "%i\t%i\t%i\t"
             "%i\t%i\t"
-            "%s\t%s\t"  # %.2f\t%.2f\t
+            "%.4f\t%.4f\t"
+            "%.4f\t%.4f\t"
             "%s\n" % (node_a.position._chr, node_a.position.pos, strand_tt[self.edges[0]._origin.position.strand],  # Pos-A
                       node_b.position._chr, node_b.position.pos, strand_tt[self.edges[0]._target.position.strand],  # Pos-B
                       dist, ("valid" if self.discarded == [] else ','.join(self.discarded)), ("circular" if self.edges[0].is_circular() else "linear"), x_onic_tt[self.xonic],  # Classification status
                       self.total_score / 2, self.total_clips, self.get_n_split_reads() / 2, self.get_n_discordant_reads() / 2,  # Evidence stats
                       len(self.edges), nodes_a, nodes_b,  # Edges and nodes stats
                       len(self.left_splice_junctions), len(self.right_splice_junctions),
-                      self.edges[0].get_entropy(), self.get_overall_entropy(),  # Entropy stats
+                      self.edges[0].get_entropy_of_alignments(), self.get_overall_entropy(),  # Entropy stats
+                      self.get_breakpoint_stddev(), self.get_breakpoint_disco_entropy(),
                       "&".join([str(edge) for edge in self.edges])))  # Data structure
 
     def get_overall_entropy(self):
@@ -1542,6 +1632,7 @@ def __str__(self):
                 "n-edges"          "\t" "n-nodes-A"         "\t" "n-nodes-B"     "\t"
                 "n-splice-junc-A"  "\t" "n-splice-junc-B"   "\t"
                 "entropy-bp-edge"  "\t" "entropy-all-edges" "\t"
+                "bp-pos-stddev"    "\t" "entropy-disco-bps" "\t"
                 "data-structure"   "\n"
                 "%s" % (''.join([str(subnet) for subnet in ordered])))
 
@@ -1710,7 +1801,7 @@ def filter_subnets(self, subnets):
             """Total of 8 reads is minimum, of which 2 must be
             discordant and the entropy must be above 0.55"""
 
-            entropy = subnet.edges[0].get_entropy()
+            entropy = subnet.edges[0].get_entropy_of_alignments()
             if entropy < MIN_SUBNET_ENTROPY:
                 subnet.discarded.append("entropy=" + str(entropy) + '<' + str(MIN_SUBNET_ENTROPY))
 

drdisco/__init__.py

@@ -28,7 +28,7 @@
     gmail dot com
 """
 
-__version_info__ = ('0', '5', '0')
+__version_info__ = ('0', '6', '0')
 __version__ = '.'.join(__version_info__) if (len(__version_info__) == 3) else '.'.join(__version_info__[0:3]) + "-" + __version_info__[3]
 __author__ = 'Youri Hoogstrate'
 __homepage__ = 'https://github.com/yhoogstrate/dr-disco'

tests/detect-intronic/test_01.out.dbed

@@ -1,2 +1,2 @@
-chr-A	pos-A	direction-A	chr-B	pos-B	direction-B	genomic-distance	filter-status	circRNA	intronic/exonic	score	soft+hardclips	n-split-reads	n-discordant-reads	n-edges	n-nodes-A	n-nodes-B	n-splice-junc-A	n-splice-junc-B	entropy-bp-edge	entropy-all-edges	data-structure
-chr21	39877811	-	chr21	42873374	+	2995563	n_discordant_reads=0<1,n_support=3<8	linear	intronic	9	6	3	0	1	1	1	0	0	1.0	1.0	chr21:39877811/39877812(-)->chr21:42873374/42873375(+):(spanning_paired_1_t:3,spanning_paired_2_t:3)
+chr-A	pos-A	direction-A	chr-B	pos-B	direction-B	genomic-distance	filter-status	circRNA	intronic/exonic	score	soft+hardclips	n-split-reads	n-discordant-reads	n-edges	n-nodes-A	n-nodes-B	n-splice-junc-A	n-splice-junc-B	entropy-bp-edge	entropy-all-edges	bp-pos-stddev	entropy-disco-bps	data-structure
+chr21	39877811	-	chr21	42873374	+	2995563	n_discordant_reads=0<1,n_support=3<8	linear	intronic	9	6	3	0	1	1	1	0	0	1.0000	1.0000	0.0000	0.0000	chr21:39877811/39877812(-)->chr21:42873374/42873375(+):(spanning_paired_1_t:3,spanning_paired_2_t:3)

tests/detect-intronic/test_02.out.dbed

@@ -1,2 +1,2 @@
-chr-A	pos-A	direction-A	chr-B	pos-B	direction-B	genomic-distance	filter-status	circRNA	intronic/exonic	score	soft+hardclips	n-split-reads	n-discordant-reads	n-edges	n-nodes-A	n-nodes-B	n-splice-junc-A	n-splice-junc-B	entropy-bp-edge	entropy-all-edges	data-structure
-chr21	39877811	-	chr21	42873374	+	2995563	valid	linear	intronic	21	12	6	3	1	1	1	0	0	0.929896694048	0.929896694048	chr21:39877811/39877812(-)->chr21:42873374/42873375(+):(discordant_mates:6,spanning_paired_1:2,spanning_paired_1_t:4,spanning_paired_2:2,spanning_paired_2_t:4)
+chr-A	pos-A	direction-A	chr-B	pos-B	direction-B	genomic-distance	filter-status	circRNA	intronic/exonic	score	soft+hardclips	n-split-reads	n-discordant-reads	n-edges	n-nodes-A	n-nodes-B	n-splice-junc-A	n-splice-junc-B	entropy-bp-edge	entropy-all-edges	bp-pos-stddev	entropy-disco-bps	data-structure
+chr21	39877811	-	chr21	42873374	+	2995563	valid	linear	intronic	21	12	6	3	1	1	1	0	0	0.9299	0.9299	0.0000	1.0000	chr21:39877811/39877812(-)->chr21:42873374/42873375(+):(discordant_mates:6,spanning_paired_1:2,spanning_paired_1_t:4,spanning_paired_2:2,spanning_paired_2_t:4)

tests/detect-intronic/test_03.out.dbed

@@ -1,2 +1,2 @@
-chr-A	pos-A	direction-A	chr-B	pos-B	direction-B	genomic-distance	filter-status	circRNA	intronic/exonic	score	soft+hardclips	n-split-reads	n-discordant-reads	n-edges	n-nodes-A	n-nodes-B	n-splice-junc-A	n-splice-junc-B	entropy-bp-edge	entropy-all-edges	data-structure
-chr21	39817544	-	chr21	42880007	+	3062463	n_discordant_reads=0<1,n_support=5<8	linear	intronic	15	10	5	0	1	1	1	0	0	0.827729376771	0.827729376771	chr21:39817544/39817545(-)->chr21:42880007/42880008(+):(spanning_paired_1:5,spanning_paired_2:5)
+chr-A	pos-A	direction-A	chr-B	pos-B	direction-B	genomic-distance	filter-status	circRNA	intronic/exonic	score	soft+hardclips	n-split-reads	n-discordant-reads	n-edges	n-nodes-A	n-nodes-B	n-splice-junc-A	n-splice-junc-B	entropy-bp-edge	entropy-all-edges	bp-pos-stddev	entropy-disco-bps	data-structure
+chr21	39817544	-	chr21	42880007	+	3062463	n_discordant_reads=0<1,n_support=5<8	linear	intronic	15	10	5	0	1	1	1	0	0	0.8277	0.8277	0.0000	0.0000	chr21:39817544/39817545(-)->chr21:42880007/42880008(+):(spanning_paired_1:5,spanning_paired_2:5)

tests/detect-intronic/test_04.out.dbed

@@ -1,2 +1,2 @@
-chr-A	pos-A	direction-A	chr-B	pos-B	direction-B	genomic-distance	filter-status	circRNA	intronic/exonic	score	soft+hardclips	n-split-reads	n-discordant-reads	n-edges	n-nodes-A	n-nodes-B	n-splice-junc-A	n-splice-junc-B	entropy-bp-edge	entropy-all-edges	data-structure
-chr21	39817544	-	chr21	42880007	+	3062463	n_discordant_reads=0<2,n_support=7<12	linear	intronic	19	14	7	0	2	1	2	0	0	0.827729376771	0.796453035938	chr21:39817544/39817545(-)->chr21:42880007/42880008(+):(spanning_paired_1:5,spanning_paired_2:5)&chr21:39817544/39817545(-)->chr21:42879876/42879877(+):(spanning_singleton_1_r:2,spanning_singleton_2_r:2)
+chr-A	pos-A	direction-A	chr-B	pos-B	direction-B	genomic-distance	filter-status	circRNA	intronic/exonic	score	soft+hardclips	n-split-reads	n-discordant-reads	n-edges	n-nodes-A	n-nodes-B	n-splice-junc-A	n-splice-junc-B	entropy-bp-edge	entropy-all-edges	bp-pos-stddev	entropy-disco-bps	data-structure
+chr21	39817544	-	chr21	42880007	+	3062463	n_discordant_reads=0<2,n_support=7<12	linear	intronic	19	14	7	0	2	1	2	0	0	0.8277	0.7965	0.0000	0.0000	chr21:39817544/39817545(-)->chr21:42880007/42880008(+):(spanning_paired_1:5,spanning_paired_2:5)&chr21:39817544/39817545(-)->chr21:42879876/42879877(+):(spanning_singleton_1_r:2,spanning_singleton_2_r:2)

tests/detect-intronic/test_05.out.dbed

@@ -1,2 +1,2 @@
-chr-A	pos-A	direction-A	chr-B	pos-B	direction-B	genomic-distance	filter-status	circRNA	intronic/exonic	score	soft+hardclips	n-split-reads	n-discordant-reads	n-edges	n-nodes-A	n-nodes-B	n-splice-junc-A	n-splice-junc-B	entropy-bp-edge	entropy-all-edges	data-structure
-chr21	39817544	-	chr21	42880007	+	3062463	n_discordant_reads=0<2	linear	exonic	247	170	85	0	5	2	4	1	0	0.811127845003	0.836571490862	chr21:39817544/39817545(-)->chr21:42880007/42880008(+):(spanning_paired_1:65,spanning_paired_2:65,spanning_singleton_1:2,spanning_singleton_1_r:3,spanning_singleton_2:2,spanning_singleton_2_r:3)&chr21:39817544/39817545(-)->chr21:42879876/42879877(+):(spanning_paired_1:6,spanning_paired_1_t:1,spanning_paired_2:6,spanning_paired_2_t:1,spanning_singleton_1_r:2,spanning_singleton_2_r:2)&chr21:39817544/39817545(-)->chr21:42878371/42878372(+):(spanning_paired_1:1,spanning_paired_1_t:1,spanning_paired_2:1,spanning_paired_2_t:1,spanning_singleton_1_r:1,spanning_singleton_2_r:1)&chr21:39846044/39846045(-)->chr21:42879876/42879877(+):(spanning_paired_1:2,spanning_paired_2:2)&chr21:39817544/39817545(-)->chr21:42876293/42876294(+):(spanning_paired_1:1,spanning_paired_2:1)
+chr-A	pos-A	direction-A	chr-B	pos-B	direction-B	genomic-distance	filter-status	circRNA	intronic/exonic	score	soft+hardclips	n-split-reads	n-discordant-reads	n-edges	n-nodes-A	n-nodes-B	n-splice-junc-A	n-splice-junc-B	entropy-bp-edge	entropy-all-edges	bp-pos-stddev	entropy-disco-bps	data-structure
+chr21	39817544	-	chr21	42880007	+	3062463	n_discordant_reads=0<2	linear	exonic	247	170	85	0	5	2	4	1	0	0.8111	0.8366	0.0000	0.0000	chr21:39817544/39817545(-)->chr21:42880007/42880008(+):(spanning_paired_1:65,spanning_paired_2:65,spanning_singleton_1:2,spanning_singleton_1_r:3,spanning_singleton_2:2,spanning_singleton_2_r:3)&chr21:39817544/39817545(-)->chr21:42879876/42879877(+):(spanning_paired_1:6,spanning_paired_1_t:1,spanning_paired_2:6,spanning_paired_2_t:1,spanning_singleton_1_r:2,spanning_singleton_2_r:2)&chr21:39817544/39817545(-)->chr21:42878371/42878372(+):(spanning_paired_1:1,spanning_paired_1_t:1,spanning_paired_2:1,spanning_paired_2_t:1,spanning_singleton_1_r:1,spanning_singleton_2_r:1)&chr21:39846044/39846045(-)->chr21:42879876/42879877(+):(spanning_paired_1:2,spanning_paired_2:2)&chr21:39817544/39817545(-)->chr21:42876293/42876294(+):(spanning_paired_1:1,spanning_paired_2:1)

tests/detect-intronic/test_08.out.dbed

@@ -1,2 +1,2 @@
-chr-A	pos-A	direction-A	chr-B	pos-B	direction-B	genomic-distance	filter-status	circRNA	intronic/exonic	score	soft+hardclips	n-split-reads	n-discordant-reads	n-edges	n-nodes-A	n-nodes-B	n-splice-junc-A	n-splice-junc-B	entropy-bp-edge	entropy-all-edges	data-structure
-chr21	39817544	-	chr21	42880007	+	3062463	valid	linear	intronic	24	14	7	5	2	1	2	0	0	0.827729376771	0.907019018116	chr21:39817544/39817545(-)->chr21:42880007/42880008(+):(spanning_paired_1:5,spanning_paired_2:5)&chr21:39817544/39817545(-)->chr21:42879876/42879877(+):(discordant_mates:10,spanning_singleton_1_r:2,spanning_singleton_2_r:2)
+chr-A	pos-A	direction-A	chr-B	pos-B	direction-B	genomic-distance	filter-status	circRNA	intronic/exonic	score	soft+hardclips	n-split-reads	n-discordant-reads	n-edges	n-nodes-A	n-nodes-B	n-splice-junc-A	n-splice-junc-B	entropy-bp-edge	entropy-all-edges	bp-pos-stddev	entropy-disco-bps	data-structure
+chr21	39817544	-	chr21	42880007	+	3062463	valid	linear	intronic	24	14	7	5	2	1	2	0	0	0.8277	0.9070	0.0000	0.9398	chr21:39817544/39817545(-)->chr21:42880007/42880008(+):(spanning_paired_1:5,spanning_paired_2:5)&chr21:39817544/39817545(-)->chr21:42879876/42879877(+):(discordant_mates:10,spanning_singleton_1_r:2,spanning_singleton_2_r:2)

tests/detect-intronic/test_09.out.dbed

@@ -1 +1 @@
-chr-A	pos-A	direction-A	chr-B	pos-B	direction-B	genomic-distance	filter-status	circRNA	intronic/exonic	score	soft+hardclips	n-split-reads	n-discordant-reads	n-edges	n-nodes-A	n-nodes-B	n-splice-junc-A	n-splice-junc-B	entropy-bp-edge	entropy-all-edges	data-structure
+chr-A	pos-A	direction-A	chr-B	pos-B	direction-B	genomic-distance	filter-status	circRNA	intronic/exonic	score	soft+hardclips	n-split-reads	n-discordant-reads	n-edges	n-nodes-A	n-nodes-B	n-splice-junc-A	n-splice-junc-B	entropy-bp-edge	entropy-all-edges	bp-pos-stddev	entropy-disco-bps	data-structure

tests/detect-intronic/test_10.out.dbed

@@ -1 +1 @@
-chr-A	pos-A	direction-A	chr-B	pos-B	direction-B	genomic-distance	filter-status	circRNA	intronic/exonic	score	soft+hardclips	n-split-reads	n-discordant-reads	n-edges	n-nodes-A	n-nodes-B	n-splice-junc-A	n-splice-junc-B	entropy-bp-edge	entropy-all-edges	data-structure
+chr-A	pos-A	direction-A	chr-B	pos-B	direction-B	genomic-distance	filter-status	circRNA	intronic/exonic	score	soft+hardclips	n-split-reads	n-discordant-reads	n-edges	n-nodes-A	n-nodes-B	n-splice-junc-A	n-splice-junc-B	entropy-bp-edge	entropy-all-edges	bp-pos-stddev	entropy-disco-bps	data-structure

tests/detect-intronic/test_11.out.dbed

@@ -1,2 +1,2 @@
-chr-A	pos-A	direction-A	chr-B	pos-B	direction-B	genomic-distance	filter-status	circRNA	intronic/exonic	score	soft+hardclips	n-split-reads	n-discordant-reads	n-edges	n-nodes-A	n-nodes-B	n-splice-junc-A	n-splice-junc-B	entropy-bp-edge	entropy-all-edges	data-structure
-chr7	151970252	+	chr21	39777764	-	inf	entropy=0.0<0.8,n_discordant_reads=0<1,n_support=1<8	linear	intronic	3	2	1	0	1	1	1	0	0	0.0	0.0	chr7:151970252/151970253(+)->chr21:39777764/39777765(-):(spanning_paired_1_t:1,spanning_paired_2_t:1)
+chr-A	pos-A	direction-A	chr-B	pos-B	direction-B	genomic-distance	filter-status	circRNA	intronic/exonic	score	soft+hardclips	n-split-reads	n-discordant-reads	n-edges	n-nodes-A	n-nodes-B	n-splice-junc-A	n-splice-junc-B	entropy-bp-edge	entropy-all-edges	bp-pos-stddev	entropy-disco-bps	data-structure
+chr7	151970252	+	chr21	39777764	-	inf	entropy=0.0<0.8,n_discordant_reads=0<1,n_support=1<8	linear	intronic	3	2	1	0	1	1	1	0	0	0.0000	0.0000	0.0000	0.0000	chr7:151970252/151970253(+)->chr21:39777764/39777765(-):(spanning_paired_1_t:1,spanning_paired_2_t:1)