align: simulate native map function returning SAM lines. #8

opencb · May 29, 2015 · bc5cd80 · bc5cd80
1 parent 468c44d
commit bc5cd80
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Showing 3 changed files with 9 additions and 2 deletions.
diff --git a/hpg-bigdata-core/native/third-party/hpg-aligner/index.c b/hpg-bigdata-core/native/third-party/hpg-aligner/index.c
@@ -1,5 +1,6 @@
 #include <stdio.h>
 #include <stdlib.h>
+#include <string.h>
 
 //----------------------------------------------------------------------------------------------------------------------
 //

diff --git a/hpg-bigdata-core/native/third-party/hpg-aligner/mapper.c b/hpg-bigdata-core/native/third-party/hpg-aligner/mapper.c
@@ -1,14 +1,19 @@
 #include <stdio.h>
 #include <stdlib.h>
+#include <string.h>
 
 //----------------------------------------------------------------------------------------------------------------------
 //
 //----------------------------------------------------------------------------------------------------------------------
 
 char *map(char *fastq, char *index_path) {
-    char *sam = (char *) calloc(100, sizeof(char));
+    char *sam = (char *) calloc(4000, sizeof(char));
+
     printf("libhpgaligner.so, map:\n%s\n", fastq);
-    sprintf(sam, "read1\t10\t20\t100M\tATAAATTACGGGGGAGA\nread2\t10\t20\t100M\tATAAATTACGGGGGAGA\n");
+    strcat(sam, "1_229454865_229455276_0:0:0_0:0:0_0\t83\t1\t229455177\t60\t100M\t=\t229454865\t-412\tAGTGCTATTTGGATTCATCCCATATGGGCCCCATCTTGTGGTCTGAGGCCTGACAGGGCTCACCTGCAAGCTCGGTTCTCTGCTGTCTTTGATATGGACT\t????????????????????????????????????????????????????????????????????????????????????????????????????\tNM:i:0\tAS:i:100\tXS:i:0\n");
+    strcat(sam, "1_229454865_229455276_0:0:0_0:0:0_0\t163\t1\t229454865\t60\t100M\t=\t229455177\t412\tTTTTAATATGTTTCAGGAGTGATTGCTTCTCTGAGCTTTTTATTATTAACTACTTTAAAGTCTATAATGGCTTCTGTTGTCTTTTCCCATTAGAATTATT\t????????????????????????????????????????????????????????????????????????????????????????????????????\tNM:i:0\tAS:i:100\tXS:i:0\n");
+    strcat(sam, "1_158253648_158254152_0:1:0_0:1:0_1\t83\t1\t158254053\t60\t100M\t=\t158253648\t-505\tTGATGTGGATTTGTTACTTCTATGGTGACTCATAGACTGAAGACCTAGTGGTAGTTTATACTTCGTGCAGTTACTAAGAGTTACTATACTGTGGCAACTG\t????????????????????????????????????????????????????????????????????????????????????????????????????\tNM:i:1\tAS:i:95\tXS:i:0\n");
+    strcat(sam, "1_158253648_158254152_0:1:0_0:1:0_1\t163\t1\t158253648\t60\t100M\t=\t158254053\t505\tGTTCCTTTAATGGGAAGTTTTCTGCCAGTGTCACTTCATTTAAGACACCTTCATTCTTTTTACAACAATCACTTCCCTCCTCCAGGTTCCTCTAGCTTCA\t????????????????????????????????????????????????????????????????????????????????????????????????????\tNM:i:1\tAS:i:95\tXS:i:19\n");
     //printf("Mapping...\n%s\n%s\n...done!\n", fastq, sam);
     return sam;
 }
diff --git a/hpg-bigdata-tools/src/main/java/org/opencb/hpg/bigdata/tools/stats/read/mr/ReadAlignMR.java b/hpg-bigdata-tools/src/main/java/org/opencb/hpg/bigdata/tools/stats/read/mr/ReadAlignMR.java
@@ -30,6 +30,7 @@
 import org.apache.hadoop.mapreduce.Reducer;
 import org.apache.hadoop.mapreduce.lib.input.FileInputFormat;
 import org.apache.hadoop.mapreduce.lib.output.FileOutputFormat;
+import org.ga4gh.models.ReadAlignment;
 import org.opencb.biodata.models.sequence.Read;
 import org.opencb.hpg.bigdata.core.NativeAligner;