From 2a648fa1ea04ec334b7682fae1a3b1dea871d01e Mon Sep 17 00:00:00 2001
From: Jens Luebeck <jluebeck@ucsd.edu>
Date: Fri, 22 Mar 2024 16:50:00 -0700
Subject: [PATCH] minor changes

---
 src/AmpliconArchitect.py |  2 +-
 src/bam_to_breakpoint.py | 74 +++++++++++++++++++++-------------------
 2 files changed, 39 insertions(+), 37 deletions(-)

diff --git a/src/AmpliconArchitect.py b/src/AmpliconArchitect.py
index ea7a4ec..f6ecb60 100755
--- a/src/AmpliconArchitect.py
+++ b/src/AmpliconArchitect.py
@@ -302,7 +302,7 @@ def process(self, msg, kwargs):
                                    coverage_stats=cstats, coverage_windows=coverage_windows, downsample=args.downsample,
                                    sensitivems=(args.sensitivems == 'True'), span_coverage=(args.cbam is None), tstart=TSTART,
                                    ext_dnlist=ext_dnlist, foldback_pair_support_min=args.foldback_pair_support_min)
-logging.info("Pair support requirement: " + str(bamFileb2b.pair_support))
+logging.info("#TIME " + '%.3f\t'%(time() - TSTART) + "Pair support requirement: " + str(bamFileb2b.pair_support))
 segments = []
 
 if args.extendmode == 'VIRAL':
diff --git a/src/bam_to_breakpoint.py b/src/bam_to_breakpoint.py
index a74e78a..6918282 100755
--- a/src/bam_to_breakpoint.py
+++ b/src/bam_to_breakpoint.py
@@ -535,43 +535,44 @@ def hr(c, wlen):
 
         for hb in hb_profile:
             cov2 = copy.copy(cov)
-            for ms_iterate in range(1):
-                fi = -1
-                if len(frozen) > 0:
-                    fi = 0
-                ms = [w for w in self.meanshift(i, window_size, hb, cov2, rd_global=rd_global, h0=h0, gcc=gcc, n=n)]
-                segs = []
-                new_seg = []
-                msi = 0
-                # print 'THIS0', len(frozen), fi #, frozen[0][0][0].start
-                # for ff in range(len(frozen)):
-                #     print "THIS", ff, frozen[ff][0][0][0].start
-                while msi < len(ms):
-                    if fi >= 0 and fi < len(frozen) and ms[msi][0].start == frozen[fi][0][0][0].start:
-                        if len(new_seg) > 0 and (frozen[fi][1] % 2 == 1 or (ms[msi][1] > 0 and ms[msi -1][1] <= 0)):
-                            segs.append(new_seg)
-                            new_seg = ms[msi: msi + len(frozen[fi][0])]
-                        else:
-                            new_seg += ms[msi: msi + len(frozen[fi][0])]
-                        # segs.append(ms[msi: msi + len(frozen[fi][0])])
-                        msi += len(frozen[fi][0])
-                        fi += 1
-                        continue
-                    elif ms[msi][1] > 0 and ms[msi - 1][1] <= 0 and len(new_seg) > 0:
+            # for ms_iterate in range(1):
+            fi = -1
+            if len(frozen) > 0:
+                fi = 0
+            ms = [w for w in self.meanshift(i, window_size, hb, cov2, rd_global=rd_global, h0=h0, gcc=gcc, n=n)]
+            segs = []
+            new_seg = []
+            msi = 0
+            # print 'THIS0', len(frozen), fi #, frozen[0][0][0].start
+            # for ff in range(len(frozen)):
+            #     print "THIS", ff, frozen[ff][0][0][0].start
+            while msi < len(ms):
+                if fi >= 0 and fi < len(frozen) and ms[msi][0].start == frozen[fi][0][0][0].start:
+                    if len(new_seg) > 0 and (frozen[fi][1] % 2 == 1 or (ms[msi][1] > 0 and ms[msi -1][1] <= 0)):
                         segs.append(new_seg)
-                        new_seg = []
-                    new_seg.append(ms[msi])
-                    msi += 1
-                if len(new_seg) > 0:
-                   segs.append(new_seg)
-                cov2 = copy.copy(cov[:n])
-                covi = n
-                for msi in range(len(segs)):
-                    s = segs[msi]
-                    c = np.average([cc[1] for cc in cov[covi: covi + len(s)]])
-                    cov2 += [(ss[0], c) for ss in segs[msi]]
-                    covi += len(segs[msi])
-                cov2 += cov[-n:]
+                        new_seg = ms[msi: msi + len(frozen[fi][0])]
+                    else:
+                        new_seg += ms[msi: msi + len(frozen[fi][0])]
+                    # segs.append(ms[msi: msi + len(frozen[fi][0])])
+                    msi += len(frozen[fi][0])
+                    fi += 1
+                    continue
+                elif ms[msi][1] > 0 and ms[msi - 1][1] <= 0 and len(new_seg) > 0:
+                    segs.append(new_seg)
+                    new_seg = []
+                new_seg.append(ms[msi])
+                msi += 1
+            if len(new_seg) > 0:
+               segs.append(new_seg)
+            cov2 = copy.copy(cov[:n])
+            covi = n
+            for msi in range(len(segs)):
+                s = segs[msi]
+                c = np.average([cc[1] for cc in cov[covi: covi + len(s)]])
+                cov2 += [(ss[0], c) for ss in segs[msi]]
+                covi += len(segs[msi])
+            cov2 += cov[-n:]
+
             ci = n
             frozen = []
             cpi = n
@@ -776,6 +777,7 @@ def get_meanshift(self, i, window_size0=10000, window_size1=300, gcc=False):
                 msr.append(msi)
         else:
             msr = self.meanshift_refined(i, window_size0=window_size0, window_size1=window_size1, gcc=gcc)
+            logging.debug('\tWriting ' + file_name)
             msfile = open(file_name, 'w')
             msfile.write('#chrom\tstart\tend\tcn\tstart_refined\tend_refined\n')
             for ms in msr: