Creation of a test to read bam with gpu

exo_bam_gpu.py

+import pysam
+seq_inf= {}
+
+
+samfile = pysam.AlignmentFile("/home/theo/Documents/alternance/Projet Alternance/dijex8000.bam", "rb")
+for read in samfile.fetch(until_eof=True):
+    seq_id=read.query_name
+    chro=read.reference_name
+    start=read.reference_start
+    lenght=read.query_length
+    end =read.reference_end
+
+    seq_inf[chro]={}
+    seq_inf[chro].append({"seq_id" : seq_id, "start" : start, "end" : end, "lenght" : lenght, })
+
+samfile.close()
+
+def depth_function(data):
+    for chro, data in seq_inf.items():
+    depth = [0] * [-1]["end"] +1 #on crée une liste qui stock la profondeur de chaque chromosome. On prend la dernière position lue de chaque dictionnaire. On rajoute +1 parce que ça compte à partir de 0.
+        for position in range(start, end +1):
+            depth[position] += 1
+depth_function(seq_info)
+