From bc5cd8077f9f35fafef1867aa6315cc0236c99a6 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Joaqu=C3=ADn=20T=C3=A1rraga=20Gim=C3=A9nez?= Date: Fri, 29 May 2015 09:15:50 +0200 Subject: [PATCH] align: simulate native map function returning SAM lines. #8 --- hpg-bigdata-core/native/third-party/hpg-aligner/index.c | 1 + hpg-bigdata-core/native/third-party/hpg-aligner/mapper.c | 9 +++++++-- .../hpg/bigdata/tools/stats/read/mr/ReadAlignMR.java | 1 + 3 files changed, 9 insertions(+), 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 index 11d55808..24531f5b 100644 --- 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 #include +#include //---------------------------------------------------------------------------------------------------------------------- // diff --git a/hpg-bigdata-core/native/third-party/hpg-aligner/mapper.c b/hpg-bigdata-core/native/third-party/hpg-aligner/mapper.c index ffb566dc..eba2c04b 100644 --- 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 #include +#include //---------------------------------------------------------------------------------------------------------------------- // //---------------------------------------------------------------------------------------------------------------------- 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 index 2cdddb7c..0837c38a 100644 --- 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;