Commit 830313ac by Eric Coissac

Tag version 1.0.3

parent 9cd4c328
1.0.1 1.0.3
\ No newline at end of file \ No newline at end of file
...@@ -472,14 +472,14 @@ cdef class StemIterator: ...@@ -472,14 +472,14 @@ cdef class StemIterator:
if circle: if circle:
minabs = min(abs(i) for i in cc) minabs = min(abs(i) for i in cc)
print(minabs,file=sys.stderr) # print(minabs,file=sys.stderr)
if minabs in cc: if minabs in cc:
first = minabs first = minabs
print("in",file=sys.stderr) # print("in",file=sys.stderr)
else: else:
# first = sons(graph,-minabs).pop() # first = sons(graph,-minabs).pop()
first = -minabs first = -minabs
print("out",file=sys.stderr) # print("out",file=sys.stderr)
nn = first nn = first
path=[first] path=[first]
lsequence=[] lsequence=[]
......
...@@ -193,7 +193,7 @@ cpdef AsmbGraph tango(Assembler self, ...@@ -193,7 +193,7 @@ cpdef AsmbGraph tango(Assembler self,
if progress and (icycle % 50)==0 and sys.stderr.isatty(): if progress and (icycle % 50)==0 and sys.stderr.isatty():
print("%s : %d bp [%4.1f%% fake reads; Stack size: %8d / %6.2f %d Gene: %s " % (wheel[(icycle//10) % 4], print("%s : %d bp [%4.1f%% fake reads; Stack size: %8d / %6.2f %d Gene: %s " % (wheel[(icycle//10) % 4],
len(graph)/2, int(len(graph)//2),
float(fake)/(len(graph)+1)*200., float(fake)/(len(graph)+1)*200.,
len(seeds), len(seeds),
growing, growing,
...@@ -205,11 +205,11 @@ cpdef AsmbGraph tango(Assembler self, ...@@ -205,11 +205,11 @@ cpdef AsmbGraph tango(Assembler self,
lgraph = graph.nodeCount() lgraph = graph.nodeCount()
if logger is not None and lgraph!=lastprint and lgraph % 20000==0: if logger is not None and lgraph!=lastprint and lgraph % 20000==0:
lastprint=lgraph lastprint=lgraph
logger.info("%d bp [%4.1f%% fake reads; Stack size: %8d / %6.2f %d Gene: %s " % (lgraph//2, logger.info("%d bp [%4.1f%% fake reads; Stack size: %8d / %6.2f %d Gene: %s " % (int(lgraph//2),
float(fake)/(lgraph+1)*200., float(fake)/(lgraph+1)*200.,
PyList_GET_SIZE(seeds), int(PyList_GET_SIZE(seeds)),
growing, growing,
delta, int(delta),
lastgene)) lastgene))
......
...@@ -199,7 +199,6 @@ def run(config): ...@@ -199,7 +199,6 @@ def run(config):
logger=config['orgasm']['logger'] logger=config['orgasm']['logger']
output = getOutput(config) output = getOutput(config)
if not pathlib.Path(output+'.gml').is_file(): if not pathlib.Path(output+'.gml').is_file():
logger.error("No assembly graph available") logger.error("No assembly graph available")
sys.exit(1) sys.exit(1)
......
major = 1 major = 1
minor = '0' minor = '0'
serial= '1' serial= '3'
version = "%d.%s.%s" % (major,minor,serial) version = "%d.%s.%s" % (major,minor,serial)
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